So, this is again an advice that should be obvious for anyone, bold
enough to delete parts of the file system, that can result in system
breakage.

There is a betwitched command, tar, that can be used to create
archives of any directory. So, the obvious action to me is, make a
tar.gz archive before deleting any system directory. That way, you
will be empowered with recovery in the ill fated event of breakage. In
the event of boot failure you can use the backup (.tar.gz) file to
repair the damage restoring bootability.