Configuration files are often modified in a live system. But the modifications are lost when the system is upgraded.

I recommend updating the excellent upgrade guide FAQ #2594 to add reference to this issue. The issue is further described in FAQ #4134.

An additional argument could be made for a utility to run prior to upgrade that ran through the server folders and noted any ".settings" and ".config" files that had changed since the last upgrade. (Further option would be for the utility to rename them so the installer wouldn't delete them prior to the upgrade.)