I'm not sure what you mean by "disabled"--do you mean not even winecfg will open? Or do you mean that now your other program won't start? If the latter--had you set any dll overrides previously? You may have just removed one that the other program needed.
The easiest solution may be to start over with a clean wineprefix:
Code:
mv ~/.wine{,.backup}
wineboot
The first command renames your .wine directory to .wine.backup (in case you want to get it back), the second will force creation of a new .wine directory. You will then have to reinstall your program(s).
