I've been doing a multiplayer playthrough with the goal of collecting every colored pearl, and have run into multiple different issues with the location of pearls updating properly between hibernations.

There are two main issues, which happen seemingly at random after hibernating: pearls sometimes duplicate, and pearls sometimes will teleport to a shelter they were previously stored in.

Players other than the host storing pearls in their stomach seems to make these issues more likely to happen, but they have still been happening while making sure to drop everything on the floor before hibernating. The issues seemed to happen more frequently as the number of pearls we kept in one location increased.

The duplication is a little annoying at worst, or even helpful at best, but the teleporting has made us backtrack constantly and in one instance caused us to completely lose track of a pearl which was in the same shelter as us moments before disappearing.