I have been playing with this mod for years, and I love this mod, but it has been a little quirky, at least as of late. I can't give you an exact timeline of events to say if its related to a specific version, but I have had issues with dealing with items on a minimal scale.

Today, I was going through my cloud chest, when a handful of concrete colors (there were like 8 of them, all in the single digits) disapeared, leaving about half of them left. I can't purposefully recreate this, but I think this issue might have come up in other ways as well, making me nervious about the mod being able to be reliable to accurately store every last block without destroying any. I've also had issues where on a different world I had a stack of anvils that would not deplete no mater how many anvils I took from the stack. It would always go back to 64. I do always have my cloud chests at max capacity with 128 chests floated up with balloons, so idk if that has anything to do with it (or what a "healthy" limit might be)

To be fair, I don't exactly play normal survival Minecraft. I go on Minecraft maps, tear stuff down in large quantities, store the loot in these chests, and then take them out to either be traded with custom villagers or be packed into Shulker boxes to then be taken other colored Cloud chests. This issue might have also been related to the Inventory Profiles Next mod, which adds a lot of inventory managment hotkeys. One of these was the scroll wheel taking items out one at a time, not great with a chest with a side bar. I have since figured out how to disable it, so maybe that was the issue, but I figured I should report this all the same. I think there is a similar issue already reported on Multiplayer as well.

I don't know what documentation I can give to help you fix this bug easier, but if it happens again, I'll be sure to let you know.