Problem with shards in inventory

I came to this reddit because Shuffle seems very knowledgeable about this game and I want him or anyone else to help me with this problem. I play darkest dungeon on Xbox and I keep getting a problem during my endless runs. Even without mercenaries I lose a bunch of shards when I end the run and go back to the estate. I think all the shards in my inventory just don’t appear when I end the run, even if I do it in a safe room between fights. The most frustrating run was I got over 500 kills and most of my inventory slots were full of 99 stacks of shards plus I was using both shard boosting trinkets and when I got back to the hamlet and should’ve gotten over 1,000 I got like 600. Can someone explain exactly how the farmstead calculates shards please?