Problem: Site was migrated to a new server but instead of migrating the entire Moodledata folder, they just migrated the filedir folder which they then stuck within the Moodle folder. Site has been semi-functional for a few weeks but with lots of issues (missing or corrupt files, cannot perform backups, permisssion issues, etc.). Site is currently on 2.2 and I am planning to upgrade to 2.6
Solutions so far: Luckily only three courses within the site. We have reuploaded files to fix corrupted links. Fixed permissions so that site does at least function for the most part. I have moved the filedir to a clean Moodledata folder that is outside of the Moodle folder and redirected config.php. Site is up and functional though still cannot run course backups as it is looking for non-existent files still. Not sure about that part, wondering if only part of the filedir was brought over?
Question: If I upgrade the site as is, will the upgrade recreate the necessary folder structure and files that are missing from my Moodledata folder (I think it should)? How strong is the possibility of destroying the site altogether (I am concerned about have empty session folder etc..)? If I am able to find the missing Moodledata folder, can I reimport it and will the site be ok despite the fact that it has been running a couple of weeks without this folder?
Would appreciate any advice. Not sure that the original Moodledata folder still exists, server guy is not comfortable about being able to restore if I break something(!) and I do not want to lose anything!