[rkomar]

It has been a few weeks since I tried firmware 5.4 and ran koreader, but last I checked, it starts up its own file chooser so that you can pick a book to read. The "file chooser" in the system is the Library application. Deleting koreader should not affect the Library application.

To get rid of the koreader icon, you also have to delete the applications/koreader.app file. The reason you go back to the home screen when running koreader is that it fails to run because you've deleted the applications/koreader/ directory.

I don't know what advice to give on WindowsDefender since I don't use it. Perhaps it has a setting that allows you to tell it what filesystems to ignore when checking.