I managed to solve the issue. I write here what I did, in case anybody needs this in the future.
I tried to run uninstaller in 3 different ways:
- Copying KFMon-Uninstaller.zip to root and rebooting
- Copying contents of KFMon-Uninstaller.zip (=KoboRoot.tgz) to root and rebooting
- Copying contents of KoboRoot.tgz to root and rebooting
I could notice anything happening after these 3 attempts.
So finally I unzipped contents of KFMon-v1.4.4-32-g3f9f34d.zip to root directory and it updated automatically, making Koreader finally work.