Let me explain what happens with those side quests during the big battle sequence. Once you reach that critical point in the main story, you'll temporarily lose access to most side activities (this is actually by design, to keep the story's momentum going). The good news is that it's not permanent you’ll get back to exploring soon enough.

Speaking of exploring, the fortress area itself has some really interesting side content that unlocks when you first arrive there in the late game. You’ve got quests like the bastion, where you’ll need keira’s magic lamp to investigate some ruins (always worth checking those corners carefully), and several others like the witchers' forge, berengar’s blade, greenhouse effect, and monster slayer. These aren’t just simple fetch quests they actually add some nice depth to the fortress’s history.

Here’s something worth keeping in mind if you’re approaching the isle of mists in the main story, that’s your big warning flag to wrap up any unfinished business (because some quests can become permanently unavailable after). The battle itself is meant to be this focused, intense experience, which is why they temporarily restrict your freedom, but don’t worry once it’s done, you can get right back to exploring and finishing up those remaining side quests.