1/ the problem is probably with you existing roles and sharing rule. the Marketo sync user does not has access to the record and therefore Marketo cannot "see" this record and sync it.
2/ Sync the record from SFDC to Marketo. This will create a duplicate in Marketo that you can merge there. If you have many, consider a automated merge tool. There are quite a few in the launchpoint. Marketo also has it's own offering. Contact Jep Castelein for this.
3/ your Marketo data is lost forever (mainly activities and program membership). But you can sync the record back from SFDC to Marketo. That will create a new record in Marketo.
The sync that was connected and then disconnected can lead to many of these touchy situations. Once the sync is back in place, you will probably need a strong dedupe solution.