This is one of the problems with JSGME that gets gamers into trouble........removing "Activated" mods out of sequence of their order of activation. The fact that the mod is greyed out means its files have been over written by another mod (and you agreed to it when JSGME asked). However, in many cases you can remove the mod anyway, leaving JSGME to lose tract of which file belongs to which mod. In your problem, your left with JSGME not knowing what to do, so it does nothing.
Always remove mods in the order they were added....."Last one in, First one out".
ALWAYS!
After having one of these types of issues, when you do get the mods out of the game, you'll need to run a "Compare Snapshot" of your SH4 game files to see if anything was left behind. This of course is only if you took a clean install "Snapshot" of your game files BEORE you added any mods to the game. If that isn't the case, plan on a complete reinstall of the game; adding a fresh JSGME (this time with a "Snapshot" taken); and a wiser way of handling the mods you add/remove from the game.
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The HMS Shannon vs. USS Chesapeake outside Boston Harbor June 1, 1813
USS Chesapeake Captain James Lawrence lay mortally wounded...
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.."tell the men to fire faster, fight 'till she sinks,..boys don't give up the ship!"
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