If they're both running the same level of the modeling code, and if you export from the FM3 to the FM9 there should be none, assuming that you haven't set a global EQ or another global setting uniquely on the FM9. Currently, the FM3 system is in beta, so there might be very small differences until they sync again.
BTW, the FM9 and FM9T are identical as far as functionality so it's superfluous to call it FM9T. There are very few times we need to make a distinction between them.