The instance system has changed quite a bit since launch really. Persistent instances were implemented during the EoF expansion and are now the norm. It's generally older instances that have just plain lockouts, which are annoying and always were for reasons similar to what you've described.
I can't think of any exceptions to the current rule, honestly. For any RoK or TSO instance, once you enter there is a short timer (30 minutes) during which you are locked to that instance. If the situation below occurrs, you can zone back in and you will be in the same version of the instance you had created. After that 30 minutes you can make a new one. If you kill a named or harvest a shiny or in some cases just kill trash you are locked to that version of the instance for the minimum duration which in TSO is 18 hours. You can come and go as you please for the next 3 days. (1 day, 11 hours IIRC for RoK heroic instances, longer for places like EH and VP.)
Curious what zone it was.