IIRC the mysql extension still overwrites files on installation, which will happen after restore of backup... would be good to have an updated version, which checks for files and doesn't copy them over, if there are already some in place.
until that is the case you can store and dump your database in a separate archive like backup.tar.gz, put it on /mnt/hda1/ and restore it from /opt/bootsync.sh like
mysqladmin shutdown
tar xzf backup.tar.gz -C /
mysqld_multi start 1