Convert characters, rather than replacing them outright. Start by explaining to them that the characters need to all be built under the same system as each other for the game to be able to function as such.
Have them rebuild the same character under the new rules. For most characters this is pretty straightforward (Pathfinder was specifically designed with this in mind), though it will require some homebrewing in the case of mechanics that don't have PF counterparts, such as Incarnum.
If characters are of different levels, you can usually simply start the game at the level of the highest-level character coming in, and give out to everyone else enough xp to raise them to that level (and gold commensurately). Simply write off the advancement as the result of adventures and experiences the characters had off-stage between their last campaign and this one (and encourage them to elaborate on those adventures in backstory).