I ran into the same issue. Just moved everything to a couple of NAS and thought I'd let the Synology box do the Mysql (it uses a fork 'MariaDb').
After reviewing a couple of helpful guides I set it up and had difficulty with the share privileges (used SMB). When I edited "sources.xml" to insert user:password for the paths, I also replaced the server-name with the IP addresses.
Everything went fine. Mysql loaded up with movies and tv shows and everything played well. I added new stuff the next day and it updated fine. Then I made a new Share and moved old Series to it for a simpler back up task. I ran Update and Clean and encountered the same problem as others. The update seemed to work but clean asked if I wanted to keep or remove each of the shares it just accessed.
After reviewing the logs I made to contribute to this thread I noticed that the new share (with the old stuff videos) worked fine.
It did use Server-name in place of literal IP address. Replaced my "192.168.1.xx" with the server-names in "sources.xml' and the
clean went thru without a hitch.
http://xbmclogs.com/pqukcxmie With problem Cleaning
After editing Sources.xml to this
Code:
<source>
<name>TV_Series</name>
<path pathversion="1">smb://username:password@myNAS/TV_Series/</path>
<allowsharing>true</allowsharing>
</source>
In place of the wrong one below
Code:
<source>
<name>TV_Series</name>
<path pathversion="1">smb://username:[email protected]/TV_Series/</path>
<allowsharing>true</allowsharing>
</source>
I finally got it to clean properly
http://xbmclogs.com/pdxqf8ro1 success !
things I learned ..
1. sometimes literal ip is not as good as trusting the DNS
2. don't forget your mysql root password if you change it as you should. It's a pain to reset
3. remember to check other Kodi installs are on the same version before you point it at your new centralized Database :-)
4. backup mysql database soon. The restore saved me tonnes of time.
5. Exporting Separate Library info may add clutter to folders but saves time in the long run.
Hopefully it'll help others.