If I remember rightly, the WC2 pilot transfer only works on savegames from the main WC1 campaign (VEGA) and once you transfer your pilot to SM1 or SM2 using the KS transfer program, you can no longer transfer the pilot into WC2.
However, Ii remember someone mentioning that there is a WC1 savegame editor flying about which allows you to alter your pilots campagin, I have yet to look for it, so can't point you there I'm afraid. Theoretically, you should be able to use the editor to make your pilot a WC1 Vega pilot and then transfer normally at the beginning of WC2.