Always make a snapshot by clicking the button/hyperlink in JSGME.
Sounds like you have 'Mod Soup'. If so, this requires a re-install
If everyone used the method of installing SH4 and Never playing it, and making a copy of the install and play that, they would have a backup to replace their Mod Soup.
Rockin Robbins made a tutorial on how to do this in Linux but it is pretty much the same procedure with Windows.
Watch this first to get the concept:
How to make independent game installations and never have to reinstall SH4 again
http://www.subsim.com/radioroom/showthread.php?t=228505
Bare bones essential mods needed post #1
http://www.subsim.com/radioroom/show...56&postcount=1
That's how you avoid a re-install in the future.
I never play my install. I use Multi-SH4 and play the copies. That way it is simple to replace the install. I haven't had to re-install for years because I play the copy's, I never play my original 'clean' install.
Here's the tutorial. Start on post #27, on page 2 (on my display) - you'll find it, then post 31, next #32, then 36, and #38:
Let's Install Linux on Moonlight's Spare Computer!
http://www.subsim.com/radioroom/show...=228072&page=2
Go through the topic - they're all on YouTube
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Bare bones essential mods needed post #1
http://www.subsim.com/radioroom/show...56&postcount=1
That's how you avoid a re-install in the future.
Sorry for the bad news, good luck. I guarantee that if you use this method you will never need to re-install again. All this time watching video's will pay off in the future so you might as well get it over with and watch them.