Can you miss the chance to achieve 100%?

So yesterday I had a quest (a white rather than a yellow marker) that was leading me again to Sarahs tombstone. I think it was called "I shouldn't have come here" or something like that. I continued a few main story missions and ended up at Lost Lake. When I by then considered heading back to make that mentioned quest, the marker was gone.

So now I am wondering, is that quest just temporarily gone? Or should I always head to none main quests first as I otherwise will miss the chance to achieve 100%? Or is there another way to avoid missing quests if this is the case?