I think what happened is that after Charybdis flew Baltar to a safe zone, he likely left Baltar on Caprica perhaps to check on the status of other operatives in their group who had to be in on the whole plan, and after that happened, Charybdis likely realized before Baltar did that the Cylons had double-crossed them as well and that his best chance was to slip in amongst the survivors with a new identity.
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