We have an older similar post that may offer a solution.
Here is a short abbreviation:
The isolate command utilizes OSTree for isolating the changes between /etc/ and /usr/etc. Where /usr/etc/ contains the ‘previous’ state and any modifications would be held in /etc/. The isolate command would not ‘see’ any changes if the content in question was already within /usr/etc.
Can you verify that these files are not already included via the /usr/etc directory?
