If I understand you correctly,
You deleted vanilla SH3 but left the SH3 commander installed. Best option is to uninstall all files. remove all directories relating to Sh3 and familiar files.
Start over.
Install SH3 plus patches.
Duplicate the installation by coping it to another new folder call GWX or whatever.
Use MultiSH3.
re-install SH3 Commander for Vanilla SH3 first. It will ask you where the location of the folder required.
After patch SH3 commander.
Install GWX 2.0 and then updated it to 2.1 then patch it.
Update SH3 Commander for GWX 2.1
I hope it helps.:hmm:
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