Rover owners: Resetting the timing

Due to hard starts at cold I adjusted the timing on the camshaft side and it was fine. But since then I've fitted SDIs and had it remapped and its playing up again, I've bought a load of stuff from matts website (dmgrs) along with the timing pins, Due to the fuel timing being changed on the remap does this mean if I Iine both timing holes up properly it will affect the map and SDIs? I've bought them anyway as there handy for when I eventually do the belts, but didn't want to mess around with timing if it affects the remap,

Cheers

James