Some of the core information may switch, such as the STR, DEX etc.. the very early code of the 3.5 system is based on the PF (or the other way around, not really sure). The skills were once using the same code but the new pathfinder sheet has overhauled the skills and that is no longer the case. Ultimately, this is a HUUGE undertaking, if you have npcs in one system my suggestion is copy the campaign switch the system and slowly just create new npcs.. A good long time before you intend to switch..... and then at the very end.. have everyone redo their sheets from myth-weavers, pen/paper, Hero Labs,... whatever character sheet program they use. Doing it this way will limit the actual in-game down time because you'll have plenty of time to test things before the player ever start to add stuff. Expect to have problems, Especially if you want to keep your own roll templates (the pathfinder default one is god awful).