Yip. The current state of affairs is in https://www.swi-prolog.org/modified/config-files.html. If the system finds the old init file and not the new it prints a warning pointing at the linked page. I think this is now dealt with. The changes are all in the swipl-devel git. If you find issues, please report.
This is surely an improvement. It will cause some inconvenience, but not too bad as it should only break some personalization and it is fixed easily.