Seafile Server, Library Problem

We have Seafile server 6.0.8 on CentOS Linux (release 7.3.1611 x86_64)
And we got big problem with one library around 1 week ago. This library used by 14 users. All of these users use different versions of the Seafile client for Windows (5.1.4+).

One day when you start a client makes a commit, which removes several directories. The user claims that he did not remove these directories. Directories can be restored via the web GUI, but again after restarting the client deletes the directories again. This problem occurs in some users.

seaf-fsck.sh said that the library is all right.

The problems go away if we re-create a library with the same content. But this is a bad solution.
What are the solutions to this problem exist, other than rebuilding the library?

This library contains many files (4397 / 3,9 GB). May be it is root case?

To find some hints, you can first look into the library history, to find out which user or client removed the directories. Then look into that client computer for problems. Perhaps the seafile.log on that client may have useful information.