I'm not sure if every container has the same limit, but I just counted the storage container in the End of Time that you send stuff to. Each chest holds 16 rows of 5, so 80 total. The storage just kept adding more and more rows as I filled it up, so it never occurred to me that there would be a limit. Also, you would think that if there was a limit, the game would warn you about it.
Item management in this game is terrible, so I was just trying to maintain a workable inventory. So I just kept sending all the crafting materials, food, scrolls, etc. that I wasn't using to my 2 chests. Just so happens I sent a quest item to the chest that was full. There's no "backlog" in the chests and no items in any of the other furniture in the bedrooms, so I'm assuming they were just permanently deleted.
So beware! Don't make the same mistake I did. Hopefully Larian adds in a warning because as we've seen here, it's a potentially game breaking bug.