I believe that is the same thing as taking a credit for the two existing tickets and then using those credits to pay for a new ticket AUG-EWR with a connection at BOS at today's prices. Always possible that the prices have dropped, but OP advised that he purchased separate ticket to save money.

In any event, all that happens with linking is that there are notes in each PNR. If OP is delayed into BOS and a B6 GA looks, they will see that they have a passenger enroute, but even that won't likely matter.