If it cannot write to data\players, I honestly have no idea how that would screw things up, much less if it would screw things up.
Unlikely though, if it is able to create a .csg as well as a .plr files under Ant-8 pilot code, then it should be capable of reading them from there as well. (no guarantee on that though). The only way to know for sure would be to PUT them into data\players and load them up again.
But I can already tell you that the converter, still needs work. And the CSG parsing itself still needs work. Right now, only the Player Specific bits relating to the reading of (most) of the plr data and saving of that is solid.