I have FSX Deluxe and Acceleration, I have never had any problems "repairing" them. If you do the repair, do ALL the discs. Remember that FSX is most probably the RTM version, which the repair will return FSX to. Running the Acceleration disc (the 3rd disc) will bring FSX up to Acceleration/SP2. It will/should repair everything to its original order. It should not change the addon aircraft at all, because it doesn't install them in the first place.

Mark