I made the same mistake and ended up knocking my website offline for a few hours (it went back to the fresh install mode). Luckily I had a backup and managed to figure out that the missing mainfile.php was the cause of that. The problem is that once I got it back online and went to the admin area I found other glitches -- the mouse-over menus would pop up but wouldn't disappear when I moused over another button, causing the menus to overlap one another. To make matters worse, when I clicked on Preferences and chose to edit General Settings, the area beneath that link came up blank.
My gameplan was to copy my old files back onto the server, then step through the updates without deleting the wrong mainfile.php and folders on the server (I had to go from 2.0.14 to 2.0.18rc). The problem was that the server knew the upgrades had already been done so it wouldn't allow me to go through those steps again.
1) Has anyone had this problem with the admin area? If so, how did you fix it?
2) Is there any way to force the upgrade(s) to work to make sure all files and database updates were made correctly?
Any help with this would be appreciated. Thanks in advance.