filename.odb_counter.odb
Those are backups of changes made to a sheet. Those depend on the version of OO you use.
What is the downside to excluding these files from the backup, or deleting files that are more than, say, 60 days old from the last time the file was modified?
In this case it will be useless to backup.
But software could complain that it expects files to be somewhere where they are not. Might be benign, might be fatal (for that software).
Settings are often tied to the version of a software you use so a personal backup should contain only personal files. You are more likely to reinstall a newer version of Ubuntu than to restore a backup. And you can not trust a backup of ./config
from an older OS to work on a new OS.
In regards to settings:
Write down what you changed, find the equivalent command line version for that, create a script with all those changes and execute it after installing an OS. That would make it a lot more portable. Works for both a restore and reinstall of an OS. And will also work for a new OS. But you might need to update your script every new LTS :)