Hi GNUser
... I looked in /etc/tc-config and found that bootsync.sh (and therefore bootlocal.sh) (line 641) runs user's backup is restored (tc-restore.sh on line 626). ...
These were all intentional.
Because cp -ais does not clobber files, running the restore first is safe.
bootsync.sh was chosen because it blocks and runs synchronously in
the foreground. This makes it possible to link local/etc / and run any
install scripts before any of those extensions get used.
bootlocal.sh runs asynchronously in the background allowing X, your
desktop, and other apps to start, potentially creating a race condition.
... Then, before rebooting, put etc/ in /opt/.filetool.lst and do a backup: ...
Generally you only want to backup files you've modified to minimize size
and time required to run your backup (and restore).
There may be some things in /etc that should not be backed up, possibly
things like fstab and udev.
Thread may be marked as solved. ...
Done.