It seems that oned thinks the database is uninitialized, but the rest of the setup (.one/sunstone_auth etc.) does already exist. You have two possibilities:
either dump the original sqlite db, convert the dump to the MySQL format, insert the result to MySQL, and finally run “onedb fsck”,
or create a fresh installation, without any locally set up data such as ~/.one/sunstone_auth.
For my ONe cloud, i went the first way, and it worked.