Originally Posted by andrewwm

There's no question that if you skip a segment when the entire ticket is on one operating carrier that all your remaining coupons (i.e. segments) will, on most carriers, be marked as void by the system.

The airline can of course waive the right to do so, but what you wanted to do would have required reissuing of a ticket to be SFO-PHL-IND. If you skipped the segment that you were contemplating, the system would have automatically voided the rest of your ticket once you no-showed for the PHL-ABE flight and reinstating the voided coupons is usually only done in the case of error (the agent forgot to scan your boarding pass, for example).

The OP's case is different in that the operating carrier for the segment he is considering skipping and the carrier owning the eticket are not the same. Because the operating carrier cannot void the coupons on other carriers (it can only return the coupons to the holder of the eticket and mark them open - available for use), it remains an open question what will happen in his case.