On DB2 for Windows, it is usually better to unzip and extract the fixpack file, and then run the setup. Any existing instances and databases should be automatically updated.
If things are really messed up, you may need to backup your database, uninstall DB2 and re-install. When you uninstall, the databases will not be removed, so you can recatalog them after you reinstall. If recatalog does not work, then restore the backup you made.