I have fop2settings.db located in /drbd/spare/fop2/, and I update its location in /var/www/html/fop2/admin/fop2settings.db to $SQLITEDB="/drbd/spare/fop2/fop2settings.db";

Whenever I upgrade fop2, my custom entry in /var/www/html/fop2/admin/fop2settings.db reverts back to default, to /usr/local/fop2/fop2settings.db";

Is there a way to not have this happen at each upgrade?

Sorry, yes. I meant the line $SQLITEDB="/drbd/spare/fop2/fop2settings.db" doesn't survive an upgrade in /var/www/html/fop2/admin/config.php.
It reverts back to /usr/local/fop2/fop2settings.db";