It's amazing how many different answers you'll get to the same question. Ex: "You can't say you'll give it back to the qunari," "You need to do her Questioning Beliefs quest," etc.
I'd say listen to Dragon Age Wiki but I've found many instances where that site is wrong. For example it says as long as she's romanced she'll come back regardless of if the Questioning Beliefs is completed but I really don't know. I know from experience that on my first playthrough I had her over 50 friendship yet she didn't return (not romanced). Perhaps I failed to do the Questioning Beliefs quest if that matters.
About your romance, did you say "of course not" when Isabela asked if feelings were brought into the relationship? Perhaps it's not registered as a romance if you do this even though others will act like you're in a relationship. If not, then it must be a bug. For me the Isabela romance is filled with them. I first romanced Fenris and then Isabela yet Aveline thought I was with Fenris in The Long Road. Then Fenris comforted Hawke after All That Remains but Varric said I was with Isabela afterwards in Friendly Concern. The game did treat it as an Isabela romance in Act 3, but not without a codex bug that listed both the platonic and romance options for "Isabela- Last 3 years" in the same description.