After talking with about 30 officials regarding this issue, only one thing is clear. This seems to be a gray area.
Here's my take. Because the shooter of the first two FT's was not chosen by the captain and/or coach, FT's were awarded to the wrong player, therefore are unmerited and are correctable.
Re-shoot the "T" FT's, then line everybody up and shoot the foul shots.
I DON'T think you can take the results of the first two and apply them after the second two are shot. Please find in the rule book where it says that one.