No, it's only cosmetic, no game progress changes.
You can set the current quest tracker in the UI to a given quest to display in the upper corner.
What I'm referring to is at certain times, that quest tracker will revert back (visually as if you had finished the quest).
So for example, say I'm on the quest 'Defending Rumah', with the objective ' Negotiate with Threg at Madrag Kaz'. I have that set to active, and that objective is correctly displayed in the upper left hand corner.
Then, after certain segments, that upper left hand corner will default back to something like 'Emily's Independence', without me having touched it, nor completed the Defending Rumah quest.
Again, it's hard to pin down which events cause this - but I wanted to mention it to see if others had similar experiences.