this has happened to me twice and after both times swearing and cursing and threating that if I find the hacker I will strangle them I discovered it was not a hacker and it wasn't links2 fault either.

When I get close to the space limit on my server (mind you 2 different servers did this both linux) and I hit any of the links in admin including build all the server won't let me have any more space and instead of changing the link or building a new directory the server just deletes those links that I was working on.

Try deleting some of your really old backup files making sure you save the last good back up you had then uploading the last good back up into the data base and see if that doesn't work

Good Luck