You can definitely re-install it. If you go to updates, you can select the d20 system and download it. Depending on how you installed the third-party package, you may also be able to uninstall it by going to Tools -> Manage Third-Party Updates in the menu. This may allow you to not have to remove the directory.
Incidentally, is the third party package the d20 community set? If so, can you tell me what the error is?
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