There's no harm in that but it does mean that users who just want the uninstall feature either have to stick with version 3.x or pay for 4.x and a load of features they may not want. If it is, then you can carefully copy back skins and plugins, testing between to make sure that a misbehaving skin or plugin wasn't the cause of the issue in the first place. However, it seems like CleanApp is moving into the space covered by apps like Clean My Mac by adding new features.
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If Rainmeter is misbehaving for you, which might be due to some file corruption on your system, or a file "ownership" issue if you have restored Rainmeter from a backup of a different OS or computer, you might want to do a "clean" installation of Rainmeter.