[Jim Porter]

Your question depends largely on the set of rules under which you are playing.

If you're talking Major League Baseball (Official Baseball Rules) then a pinch runner would indeed be a substitute, and the first baseman would be out for the game. There is no re-entry in the OBR.

Other sets of codes allow for courrtesy runners and/or special pinch runners. Some sets of codes allow re-entry, Some rules prohibit re-entry.

So, under which rules would you like your question answered?