When does the Backup Data become different than the Configuration Data?

There could be many possible scenarios, but here is one as an example:

You check out the program from Archive (stored in the Configuration Data field) to make edits and when you check it in, you leave a local copy.

Later you make changes to the local copy, go online, and download the changed program to the controller. Now the new changes are not checked in to Archive in the Configuration Data.

The scheduled nightly backup runs creating a new backup with the updated program in the controller. This backup is different than the version stored in Archive in Configuration Data.