I was planning on running 2 black 2 white and 1 green 12 gauge wires through flex from panel to kitchen wall, then changing to rigid pvc to go under ground to kitchen island for microwave and gfi circuits but the project manager insists I use cable until I switch to pvc because of cost. I didn't realize it would save that much money and prefer not having unnecessary junction boxes. so I just thought I'd ask if there were any potential issues before doing it his way. Thank you.
In answer to the question you asked in your title. There is no issue with changing from a cable (romex) system to a conduit system just so long as it is done properly.
FYI - The difference between a cable system and a conduit system other than initial cost is that a conduit system is more flexible when it comes to upgrades, remodel or repairs. For example, you have a receptacle burn up and it also damages the conductor far enough back you can't make a splice to repair it, with a conduit system you simple go back to the next junction and pull a new conductor. If you have a cable system you will have to open the wall up to replace the cable.
Running PVC to the island and installing conduit and conductors is a good idea since it allows you the opportunity to replace or modify your circuity to the island without cutting up your finished floor. Most houses in the US are normally run in Romex because of the initial cost and electricians are trained to deal with the problems they may cause down the road.
Hope this helps.