Code the AI so that it knows to do one of three options when the Planet it's Colony Ship was headed for has been colonized:
1: As has been suggested, convert the Colony Ship to a Transport to invade
2: Change the Colony Ship's role to Explore - removes it from the now colonized planet, gets it...well....exploring for another planet to colonize.
3: Decommission the Colony Ship. More money for the AI.
All choices done depending on what AI thinks suits it's race best.