Hello beatlemanu!

Profiles photo are stored in table `media` and files - in directory 'media/images/profile'. Every user with pics has folder with name as his ID. Delete profile photos you can via admin panel->content->profile photos section. It's very interesting that "after sometime" photos are disappear. Can you check - has your server any activity in this time? May be some scripts which clear space ? Or may be disk quote exceeds?

Hello TomS!

According your trouble - it's see more not enough to delete photo files, you should delete profile photos via admin panel->content->profile photos section.

Regards