Clean video library removes existing movies

Hello,
Since I changed my video folder structure, a “clean video library” removes often movies from my database, which actually still exist.

My structure, when it works correctly (one folder that contains everything):
Movies
|- MOVIES HERE

My new structure (categorized in year range and some special genre as subfolders):
Movies
|- 1900-1999
||- MOVIES HERE
|- 2000-2005
||- MOVIES HERE

|- Family
||- MOVIES HERE

It seems that a cleanup randomly removes an entire subfolder from the database.

Kodi’s “Scan recursively” is activated for the media library.

Because I replace movies very often, I need to clean after each update. So All my database updates are followed by a cleanup every time (via Add-on:XBMC_Library_Auto_Update). And most of time, my database shrinks by 200 items after a cleanup. A further update would bring the items back, but [update cleanup update] is not a good approach and in addition scanning of 200 items takes not less time…

Someone any idea or ran into the same issue?

Issue on latest Kodi 17.1 on Win32 (Win10) and Odroid C2 and Raspberry Pi 2 (via latest Libreelec).