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Is it possible that through modding even though I used the JGME I have damaged the install?
If so, is a complete re install the only option?
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JSGME isn't perfect.
Only
you can answer this......Have you ever removed a mod out of sequence? Meaning to say, you have 4 mods "Activated" through JSGME, yet you decide to remove the Second mod in your list without removing number 4, then number 3, before getting to mod number 2? If so, you've just put JSGME into quite a fix. It does a good job in keeping track of the mods you load.....and the sequence in which you load them. It doesn't do very well when you remove mods out of sequence. Files get left behind in the main game folders causing errors and other trouble.
Call it "Operator Error" on your part!
JSGME isn't perfect, yet it has a way for you to check to see if the main game files are as they should be (JSGME developers knew it wasn't fool proof). That's with using the "Compare Snapshot" feature under JSGME's "Task's...." menu. It will compare the existing stock game files to the files of the game when you first added JSGME.
Didn't take a "Snapshot" of your brand new clean game install folders/file's as the instructions of JSGME states? You've just answered your own question.