This may be a dumb question but are you running SH3 Cmdr? If so, you might be able to perform a roll-back. If not then the only thing that I can suggest is to back up your mods then uninstall & reinstal your game. It's a pretty drastic solution but it will solve your problem. The same thing happened to me once before. I forgot
to roll-back the game before uninstalling Cobalt's mod and couldn't get the game to revert to the default skin. Fortunately SH3 Cmdr now has an "auto roll-back" feature.
Glad you were able to solve your problem.