I assume by this, you mean you have run an upgrade, Jira is now running, but when you try to log in, you get some form of error? Is that right?
On the rest of the question:
These two are files that you had customised in your old installation. The installer/upgrade program has no way to know what you might have done in them to customise your service, it can only replace them with its known-to-work defaults.
If you've followed the upgrade docs, you will have taken a backup of these files (either manually, or by letting the installer take a backup), and then, after the upgrade finishes, you compare all the changed files to see if you need to put the changes away from default you made in the old install back into the new versions.
In this case, my guess would be that you have customised a url or maybe a user system in one of those two files, and because you have not re-applied those customisations in your upgraded systems, it's not working the way you expect.
You'll need to check what was customised on the old version in those two files and see if you need to reapply it to the new ones.
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