If they're WeiDu mods, it's not too bad, if they're not, you can't uninstall them.
For WeiDu mods, look in your BG2 directory for Weidu.log, that'll list the components of the mods you've installed. provided you still have the Setup-mod.exe and SETUP-MOD.tp2 files for the mods, you can uninstall them (run Setup-mod.exe and follow the instructions).
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