Default Using link2sd on optimus f3. Changing out sd cards, need help.

Hey guys, so I decided i need to change out to a smaller sized sd card on my optimus f3. I managed to copy the partition from the old card onto the new card using Minitool partition wizard. But I have a problem. After I copied all the contents, the partitions are swapped. The 1st partition is supposed to be the partition where music and stuff go to and the 2nd is supposed to be for the apps. Well they are swapped and I dont know how to change the order of them using this program. Does anybody have any ideas?