From what I remember, the agents can only look at the current status of your application. So if something was updated, they'd not be able to look back and say "this and this was changed". What you need to know is that there's literally nothing to worry about in this. We've seen countless such cases and you can search the forum to find more and get peace of mind

There are a lot of disjointed systems in IRCC (GCKey vs PR tracker) and you can only imagine what the internal infra would be like.
About the GCKey login issue:
1. Have you tried resetting your password?
2. What type of login issue are you facing? Redirect to cic.gc.ca or 403 or 500 errors?
3. Have you been able to log into your PR tracker?