It appears that after UN-installation of some applications using installation monitoring uninstall software (like Total Unistall) something happens to Comodo FW, some application rules are lost and some of them stop working suggesting possible corruption of installation.
1- Is this a known problem ?
2- How to correct this issue short of un-install / re-install of whole CIS ?
This is not an issue with CIS.
Don’t allow any uninstall program to remove anything blindly (This includes registry cleaners).
This always leads to issues (with Windows and/or other applications/programs).
Always verify what is to be removed first.
Does CIS report it is not functioning properly? If it does can Diagnostics fix it?
If the only problem is with broken rules you can choose to repair them. In case a configuration is broken (think standard rules for Windows and CIS have vanished or are broken) you could think of importing and activating a factory default configuration and start from scratch.
In case an uninstalling or clean installing of CIS would be a problem you can use this unofficial clean up tool. In case needed run it in Windows Safe Mode.
There is nothing we can do about errors caused third party tools. All you can do is report the issues with the makers of these tools.