Issues with the Shards

Hello! I realize many people probably haven't played this game in awhile, but I'm hoping someone can help me?? 

While progressing my game to collect all the shards I ran into an old issue where shards/ocularum's either wont show up, or will tell me I've collected all avaliable shards.

I'm mainly having the issue in The Emerald Graves, where the quest is incomplete, but I've done all the Ocularums/picked up all the shards I found! 

I've put 100+ hours into this playthrough and I'd hate to lose any progress with them. Does anyone have a solution that may solve this without losing any data on this character?