Scan Missing large number of files

Hi,

I've had Ubooquity running fine for 6 months or so, it's gone down several times, both planned and unplanned and always come back up just fine. 

The other day my file server got disconnected and as the ubooquity data dirs were mounted there through CIFS in fstab ubooquity couldn't find the files. I didn't realize the file server was down and restarted ubooquity, this caused it to start wiping all the comics from the database, I stopped the process half way through when I noticed what was happening.

After I got the file server back online I restarted Ubooquity and it performed a new scan, I lost my place in the comics I was mid, which sucked, but I can live with that.

However ever since then it now randomly doesn't show almost half of the comics. It finished it's scan, I confirmed by browsing the dirs in linux directly that all the comics are there but each comic is missing almost half it's issues. So it will go 1, 2, 4, 8, 9, 10, 14, etc. No noticeable pattern like odds/evens, or files with special characters, etc.

I've since rebooted it several times, it performs the scan, says it added no new files, reports no errors, just doesn't have them.

Any ideas on how to fix?

Running in headless CentOS 7 with data dir mounted from Windows Server file share over SMV in /etc/fstab although I don't think this is related to the issue, just providing as much info as possible.