Commenting them out would be like removing the file entirely.
Removing the repository is safe and it will not affect the state of an installed package.
However, it would result in that installed package no longer receiving updates from that maintainer.
If you do not use that software or have any doubts and it is not a big deal to reinstall it, I would just clean them out and reinstall if needed.
Hello, @Aravisian
For this issue..
So, earlier I did partial upgrade from update manager.
And then It basically fixed itself.
No more broken package system.