Some files always disappear from time to time

There are many books sorted in my MarginNote3.
Recently, I find some file’s books disappear completely, but I can read them in my IPAD MarginNote3.
And it sometime reappears in MAC, and then disappears again.
In IPAD MarginNote3, there is no trouble like this.
I don’t know why, maybe it’s because Cloud, or I created so many folder in a folder. There are 13 folders in a folder or the version is free in MAC. I don’t know why, if you know how to deal with the trouble, please tell me why and how.
If I explain this trouble not clearly, please tell me what I should explain concisely or precisely.
Best regards to you.