Var folder empty data disappeared while generating thumbnails

We were re-generating thumbnails for 30k pictures since last 3 days and everything was fine and it was down to last 3.4k pictures. Today, all of a sudden the thumbnail regeneration process stopped with an error, when we ftp'd to check 'var/log', we are noticed the whole 'var' folder was empty. How can this happen? This was on Gallery 3.0.3.

We were VERY VERY lucky to be using the S3 Amazon plugin and running the site on the cloud and were able to recover the photos but now when we try to continue with that 3.5 thumbnail generation process, it displays this error - "Fatal error: Exception thrown without a stack frame in Unknown on line 0"

How to continue the process and what can be done to avoid the wipe out of contents under 'var' directory apart from taking regular backups.

Thanks,
Mick

Update-1: We upgraded our gallery to 3.5 but still not able to build the last 3.5 out of date photos. Is it possible to just clear them and do it on an individual album basis?

Update-2: We were able to generate the rest of the thumbnails by manually running an sql query i.e.
UPDATE photos.`items` SET `thumb_dirty` = '0';