I'm thinking that's not the question. The question is whether a new Moodle install based on the same login username decision (I'm guessing here, but I know it wouldn't work otherwise) would allow new accounts be recognized as an existing account when the user SSO'ed over to Mahara.
Our school district, last summer, changed the designated primary login username field for LDAP from SAMAccountName to email address (our UserPrincipalName). We ran queries against both Moodle and Mahara databases for a brute force change, and the connections were retained. (We have found some artifacts from that in Mahara -- it has several storage points for login usernames, and a few data field size problems -- but nothing that broke us.)
But we're also planning to move to Moodle 2.2 this summer, and are toying with the idea of starting from scratch. So my question would be exactly Juan's. Anyone?