A tricky question
The thing is that the only available online doc (at least we know about) is
this. If you go to page 33, you'll read particularly about Europa-Spezial Kroatien. Under part 9.2.4.7 it's stated:
Eine Fahrtunterbrechung ist unter Einhaltung der Zugbindung höchstens zweimal je Fahrtrichtung, bis maximal je unter 48 Stunden möglich. As far as we understand, it refers to the cases when you/cashier manually enter stopovers yourself prior to purchase. Also earlier (9.2.4.3) we have:
Die Fahrkarten zum Angebot „Europa-Spezial Kroatien“ gelten nur für die eingetragenen Tage und Züge (Zugbindung). Anyway, the best idea is simply to email DB directly, they tend to answer quickly and you'll definitely dispel your doubts.
Ourselves we usually do more conventional trick in order to make a stopover: when purchasing similar Europa-Spezial ticket we just enter needed stopovers and time for it, it still allows to purchase discounted ticket, but at the same time makes a stop let's say 'officially recognized' and in compliance with part 9.2.4.7
I've done that once in Slovenia, in Ljubljana I was waiting for my EC to Munich but there was a local train leaving to Jesenice one hour in advance and I've decided to see this small town before. I've just asked the ticket inspector before entering the train if I can travel to Jesenice and wait there or do I need to stay here. He looked at the ticket briefly and said sure no problem.
Did you have Spar ticket or normalpreis? Even if yes, then anyway hint about
conductor did not know/didn't care sounds rather plausible, so doubt this case can serve as any proof/example.