You won't get any miles back because DL prices awards as round trips. If you removed AUA-ATL-SFO, you'd have a one-way ticket, which prices as a round trip, i.e. the same miles you paid. How about once you make PM changing the ticket to have a stopover in ATL on the return and then just fly from ATL to CLT on a separate ticket? You could have that return to ATL and then finish up the ATL-SFO portion.