Updating to 1.9x will rebuild index when you select something in the scene. Since all the versions would be outdated then, it will rebuild everything - but, if there were some broken assets in there already, eg. which was not obvious if you didn't rebuild anything, and had no reason to rebuild anything anyway - rebuilding everything would make the already broken assets "break" properly.
Anyway, your best bet is to revert via source control / backup - you'll find that a lot of files may have changed. If you cant do that, you'll have to update to 1.9x and manually fix all the broken references in the sprite collections. Email support for more details on what you need to do, and what errors you get, etc.
The fact that you had a clash with the previous scripts suggests that the scripts may already be broken at that point? Did you at some point in the past share the project without meta files, etc? Or, that they weren't going into the right directories (did you move the installation directory?)