Gdansk to Hamburg

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I tried to book tickets online from Gdansk to Hamburg via the De Bahn web site but found that they can only post out international tickets.  As I am leaving shortly I don't expect that they'll arrive in time before my departure.  So my questions relate to the reliability of the connection in Berlin.
I can buy separate tickets online ie Gdansk to Berlin (PKP) EIC54 07:28 arr 13:43, and Berlin to Hamburg (DB) ICE 14:23 arr 16:21 (as shown on the DB website) for the same total price.  If I'm booking tickets with different companies and there is a holdup on the first leg of the journey, can I assume that our tickets for the second section won't be valid if we miss our connection?
Do you think that I should book a later Berlin-Hamburg train ie leaving at 15:06 giving me a connection time of 1hr 23min (rather than 40mins) or am I being overly cautious? 
I've used trains in Poland before that seemed to be on time, but not had to worry about connections.  I understand that I could buy the second tickets when I get to Berlin but at an extra cost.
I've tried other ticketing arrangements, to the border etc, but I still end up with the connection in Berlin.
Thanks in advance.

I tried to book tickets online from Gdansk to Hamburg via the De Bahn web site but found that they can only post out international tickets.

Yep, there is this issue with certain journeys starting abroad. It usually has to do with verification of tickets bought online by conductors from a different country 

I can buy separate tickets online ie Gdansk to Berlin (PKP) EIC54 07:28 arr 13:43, and Berlin to Hamburg (DB) ICE 14:23 arr 16:21 (as shown on the DB website) for the same total price.  If I'm booking tickets with different companies and there is a holdup on the first leg of the journey, can I assume that our tickets for the second section won't be valid if we miss our connection?

Well, it depends on the ticket type. If, as I assume, it's a discounted ticket with fixed train (so-called zugbindung), then yes, DB won't recognize delay on your previous leg in case you have separate ticket from PKP for that first leg

Do you think that I should book a later Berlin-Hamburg train ie leaving at 15:06 giving me a connection time of 1hr 23min (rather than 40mins) or am I being overly cautious?

Difficult to say, since it can be not only rail company matters, but weather, border checks, etc. But in general I would say that >40 min. delay of the "flagship" train like EIC54 is highly unlikely. Btw, you can check current delays of the same train and at least have some statistics on the matter

I understand that I could buy the second tickets when I get to Berlin but at an extra cost.

The extra cost can be more than twice (if compared 29 euro discounted ticket bought in advance to 78 euro one flexpreis bought before departure), so ouch...

I've tried other ticketing arrangements, to the border etc, but I still end up with the connection in Berlin.

Hmm, maybe you can give us the date, so that we can take a fresh look? Time interval is morning departure and afternoon arrival, right?

Thanks for your quick reply.
I'll check out the stats.  In the meantime our travel date is Tues 18 Oct. And yes, depart early morning to arr in afternoon.

I haven't had much luck finding statistics on punctuality. Thought I was onto a winner when I found this site, infopasazer.intercity.pl, (+ google translate) but nothing transpired.  PKP do seem to take punctuality seriously judging by pages 9,10,11 of their 'Regulation on on-line ticketing.....' but it still doesn't seem to cater for cross border connections.  As I understand you to say, it is up to the next train conductor.

And yes, depart early morning to arr in afternoon.

One interesting and very cheap, especially for more than one traveler, option I can think off is to avoid Berlin at all. Instead go more direct (geographically) route: Gdansk to Szczecin, then Szczecin-Bützow railway to Lubeck and finally to Hamburg with arrival more or less the same time as via Berlin. Gdansk to Szczecin ticket for the morning TLK cost 45,5 PLN (with discount for early purchase) or 91 for two. While leg from Szczecin to Hamburg you can cover with German regional (lander) ticket, thus, in case it's two passengers, making it <30 euro person for the entire trip + flexibility on German part (=no need to purchase anything in advance and possibility to make stops somewhere in Mecklenburg-Vorpommern). If it's more then two passengers, then per passenger price will be even lower

Another option, which will "secure" your change in Berlin is to go with combination of tickets, thus not Gdansk-Berlin (bought form PKP) & Berlin-Hamburg (bought from DB), but slightly more nuanced version: first you buy Polish domestic Gdansk-Poznan for the very same EC54 (now with superpromo in advance discount it's 49 PLN or 11,3 euro), then Poznan-Frankfurt (Oder) for 52 PLN (12 euro) for the same EC54 and finally Frankfurt (O) to Hamburg with change to Berlin with arrival to Hamburg with ICE 800 at 16:21 (29 euro per person or 48 for two), which is DB domestic, thus print-at-home e-ticket. This way it will be DB responsible for the change in Berlin, and in case train from Frank.(O) will be late, then you can always catch next ICE to Hamburg with a DB stamp on your ticket.

Thank you tUt.  Brilliant!!!
I've just spent the last couple of hours plotting both routes but think the regional one might be better for another journey when I have the time to plan - and perhaps when the weather will be better!
I can't believe the difference in price splitting the Gdansk route to the border.  So I'll get two domestic tickets (PKP) and the one through ticket from Frankfurt (O) to Hamburg (DB).
We are actually planning go to Lubeck for the day from Hamburg and I was going to get the Schleswig-Holstein Ticket you recommend on your web site.  I assume I can buy it on the day from Hamburg Hbf or can I get it from the local Hamburg train station (four stops I think) and use it domestically to and from the main station?  Or should I buy in advance online?  Does this ticket differ from the nah.sh web site tickets?  I'm a little confused I think....
One final question.  We are travelling on from Hamburg to Amsterdam for three days then staying one night in Rotterdam before taking the night ferry from Hoek van Holland to Harwich for a new experience!  Any tips and tricks along the way please?
Thank you very much again.  Your knowledge is invaluable.

Hi again tUt,
I've just realised that I can't stay on the EC54 at Frankfurt (O).  Well not according to DB.  So I may still have the problem of connecting, but this time at Frankfurt (O) where we'd arrive at 12:15.  DB show 12:57 RE18122 dep Frankfurt (O) arr Berlin 14:09 following on with ICE800 dep 14:23 for Hamburg.

I can't believe the difference in price splitting the Gdansk route to the border.

Well, ticket "break" via the border is one of the oldest tricks to save money, since when we speak about standard full-fare tariffs, then domestic rail tariffs in that part of Europe is much cheaper than international cross-border tariffs. 

So I'll get two domestic tickets (PKP) and the one through ticket from Frankfurt (O) to Hamburg (DB).

Gdansk-Poznan is domestic PKP (you buy it from PKP), Poznan-Frankfurt (Oder) is international, since Fra. is already in Germany (you can buy either from DB or PKP, online or ticket counter before departure... doesn't matter, since in this case price will be the same) and finally Fra.(O)-Hamburg is domestic DB. Ideally ticket "break" in this case should probably look like Gdansk-Rzepin (last Polish station), then cheap local train/bus to Slubice (polish town across the river from Frankfurt), walk from Poland to Germany over the bridge and then domestic German train to a place you need. However doing it around noon mean losing couple hours  (=later arrival to Hamburg), so that is why paying those 10+ euro for Poznan (or Rzepin)-Frankfurt (O) leg is inescapable. 

I've just realised that I can't stay on the EC54 at Frankfurt (O).  Well not according to DB.  So I may still have the problem of connecting, but this time at Frankfurt (O) where we'd arrive at 12:15.  DB show 12:57 RE18122 dep Frankfurt (O) arr Berlin 14:09 following on with ICE800 dep 14:23 for Hamburg.

That is already tricks DB website plays with you. The thing is that it searches fastest possible connection, thus offers you 12:57 departure, since, as search engine thinks, it saves you long change in Berlin. In case you want to use EC54, then you need a minor manipulation - in "More means of transport" section simply uncheck all the transport types beside EC/IC & ICE -
and then you'll get what you want -

We are actually planning go to Lubeck for the day from Hamburg and I was going to get the Schleswig-Holstein Ticket you recommend on your web site.  I assume I can buy it on the day from Hamburg Hbf or can I get it from the local Hamburg train station (four stops I think) and use it domestically to and from the main station?  Or should I buy in advance online?

You can get German LanderTickets from any ticket machine in the region. Possible to buy it at the ticket counter, but then you'll be charged extra 2 euro. Absolutely no need to buy in advance, since those tickets can't get sold out and the price is always the same.   

Does this ticket differ from the nah.sh web site tickets?  I'm a little confused I think....

Ha... in Germany there is a bit tricky situation, since besides big statewide rail company there is also dozens smaller regional transport associations. These associations not only respect DB tickets, but might have there own local integrated tariffs (meaning ones that include all types of transport in the region of this or that association). Schleswig-Holstein's story is exactly like this and the website you've mentioned indeed help passengers navigate local tariffs (but DB as well mentions it - https://www.bahn.de/p_en/view/offers/national/regional/sh-tarif.shtml ). But the best part is that ticket machines (or ticket cashiers), depending on your route will sell you cheapest option (it can be under SH tariff, or DB, or whatever else), so in fact you don't need to worry about overpaying - system will offer you best option depending on route/number of people/day of the week, etc.   

We are travelling on from Hamburg to Amsterdam for three days then staying one night in Rotterdam before taking the night ferry from Hoek van Holland to Harwich for a new experience!  Any tips and tricks along the way please?

Story with Hamburg to Amsterdam is rather banal, you should probably just go with DB discounted ticket (so-called Sparpreis Europa) bought in advance using DB website. In Netherlands (e.g. Amsterdam to Rotterdam) you kind of need to be a local to enjoy cheaper travels by train, while for foreigner on short trip it's more or less about straight forward one-way ticket with standard tariff.

All I can say is thank goodness for Europe Trains Guide!