It's very likely that your mods have made changes to official files and verifying the integrity of files will reacquire those files and replace the ones your mods modified. It's really impossible to know without knowing the mods you are running.
With that said, chances are that the issue you are experiencing is caused by your mods in the first place because this is not a known bug that affects many. The only way to be certain is to do a clean install as described here:
How do I perform a clean install of the game? — Cyberpunk 2077 | Technical Support — CD PROJEKT RED
Then try skipping to Phantom Liberty on a clean game.
Alternatively, you can go through your mods and their respective pages to see if there is any known problems/compatibility issues and potentially how to solve them.