Is this an HDD or an SSD?
Can you open Disks from the app menu. Click the menu button on the upper right side, and then select SMART Data and Self-Test
Last option listed: Overall Assessment: What status is the disk- how many bad sectors?
Honestly... If this was me...
I would back up all personal data and do a full reinstall.
What we have is a lot of Unknown on this one... If several certain software that you are aware of are now damaged- and reinstalling is no help- there may be Bigger Issues you have not seen.
It's better to have a clean start- with the warning you have now- than a catastrophe later.
You may also look into a new SSD. I do not know how old this one is and only 2 bad sectors is not really anything to fret about... But just to put the note in your future plans...
This is done automatically by the system after repair has been done - which you did earlier.
Even so, if programs are not working- you do not know what else is damaged and may not be working. It is not worth the risk.