@Deobulakenyo:
2. It won't affect your current configuration, so, yeah, as @geek1011 said, the OCP take care of everything.
3. KOReader & Plato aren't affected by *anything* (short of factory resets). KFMon *will* be disabled after a FW update, which is why there's a dedicated package for it marked "run me after FW updates"

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Patches are completely orthogonal to the whole thing.
4. Just remove their respective folders (and eventually clean up the launchers).