We are working with an oracle database in which the person that set it up is "long gone" and thus do not know the sysdba password, but need it. We have root access to the box (its on linux). Is there any way to recover or change the sys passwords?
Have you tried logging into Linux as your installed Oracle user then
sqlplus "/ as sysdba"
When you log in you'll be able to change your password.
alter user sys identified by <new password>;
Good luck :)