[rafi1]

setup is Android and Win clients with media files only on Windows (Android is using SMB).
1. sure, I'll attached the two - ATV and Win . [ I believe some of the issues, were created due to mistakes in sources capitalization , plus using   SMB on android]
    https://drive.google.com/file/d/138V2haB...sp=sharing
2. Won which system ? ATV ro Win? I was trusting my Kodi library cleaner to delete orphan entries (w/o actual files? if this is what you mean). Do you recommend to use your script too?
3. I am not sure myself. As I said above, I think the combination of Android and Win is one possible root cause, but also capitalization  mistakes during manually entering library source paths in the past. One more possible root cause is changing scrapers from time to time to improve detection (no idea why this should be a cause, tho)
4. I cannot comment on this one...

PS:
I've  read looked now into Mezzmo (free) , and can se a few benefits (mainly synching between devices). Still, I am not convinced their free version has advantage over Kodi using remote SMB file system (that Mezzmo will serve). For example - showing updated state of your file system (removed/new files).

[jbinkley60]

setup is Android and Win clients with media files only on Windows (Android is using SMB).
1. sure, I'll attached the two - ATV and Win . [ I believe some of the issues, were created due to mistakes in sources capitalization , plus using   SMB on android]
    https://drive.google.com/file/d/138V2haB...sp=sharing
2. Won which system ? ATV ro Win? I was trusting my Kodi library cleaner to delete orphan entries (w/o actual files? if this is what you mean). Do you recommend to use your script too?
3. I am not sure myself. As I said above, I think the combination of Android and Win is one possible root cause, but also capitalization  mistakes during manually entering library source paths in the past. One more possible root cause is changing scrapers from time to time to improve detection (no idea why this should be a cause, tho)
4. I cannot comment on this one...

PS:
I've  read looked now into Mezzmo (free) , and can se a few benefits (mainly synching between devices). Still, I am not convinced their free version has advantage over Kodi using remote SMB file system (that Mezzmo will serve). For example - showing updated state of your file system (removed/new files).

1.  Your source.xml file looks Ok and is only the main SMB mapping and not everything in the path table.  I think someone who is running a mixed environment with a MySQL server should provide guidance on which Kodi client to do library updates from but I think it should likely be a Windows client which isn't case sensitive. 
2.  Kodi experts will need to explain what level of cleaning that Kodi provides natively but I can say the main reason I wrote KSCleaner is to address orphans and data integrity issues that Kodi and certain Kodi library management practices leave behind.  I'd highly suggest doing a database backup and then running KSCleaner from a client.  Again, I'll defer to others who run similar setups on which client to use.  I suspect Windows.
3&4.  I need some help from Kodi experts here to understand why these two situations might be occurring.  I can certainly add some brute force path duplicate deletion capabilities to KSCleaner and then you'd likely need to run KSCleaner a second time to clean up any orphans that creates but it would be effective.   However, I think it is good to understand recommended best practices here to avoid having to continually do this level of cleaning / deletions.

Hopefully some other users or a Team Kodi person can weigh in here.

Thanks,

Jeff