Newbie question of the day :

If I have a ship with R2D2 recovering shield and a shield upgradd for a ship without shield (oor even one with shields), will R2 recover the shield from the modification, or only the shields on the base ship?

He recovers all shields, including the one from the modification.

The modification actually changes the number of shields printed on the ship card. The original value no longer exists. The modified value is the only value in existence.