Siddhant:
Your situation, that the problem started after a Windows re-install is typical. Apparently while trying to reinstate the user data, some permissions in the CryptSvc ProtectedRoots registry area are not properly reset.
AFAIK the registry repair is the only solution. If you can get to HKey_Current_User...ProtectedRoots, set the permissions so you can delete it and then delete it, you should be OK. CryptSvc will rebuild ProtectedRoots on next access and you should be OK. Keep regedit open, do some other work that requires starting a program, like close/open Chrome or Edge, refresh the regedit page and you should see the reconstructed ProtectedRoots.
You don't need to delete Root. Your business app is probably enabled through Root\Certificates and since you're not deleting Root or Certificates, the business app should not be affected.
The registry repair script here does delete Root & Certificates and then restores them, which should also be safe. If you run the script, post the logs to the script Chrome Help Forum and I'll followup there.