I'd see a lawyer ASAP. AFAIK, PA follows the same criteria for CCW as it does for firearms ownership. If you can't get a CCW, it may be that you can't legally own a firearm as well, despite passing the PICS/NICS. This of course could potentially get you into trouble if they decide to do some followup. Since you are renewing and not applying, they will only logically assume that you own firearms as well, and Philly ain't exactly a haven for gun rights. PICS records are kept indefinitely, so they can tell (presumably pretty easily) if you've made any firearms purchases from an FFL.
The piece you quoted pretty much reads verbatim from the 4473:
b. Are you under indictment or information in any court for a felony, or any other crime, for which the judge could imprison you for more than one year?
c. Have you been convicted in any court of a felony, or any other crime, for which the judge could imprison you for more than one year, even if you received a shorter sentence including probation?
Only exception mentioned here for (c.) is a state misdemeanor that is punishable by only two years or less. However, you mentioned felony, so that seemingly doesn't apply here.
I'm no lawyer, but I agree with dbrowne1. It seems like either your case is still open, they screwed up, or you misunderstood the terms of the deal. Either way, it could technically be illegal for you to have access to a firearm right now. I'd "gift" either your parents or children with all your firearms now (only way to quietly get rid of a handgun here - no private transfers of them except parent<->child) until you can talk to a lawyer and get this straightened out.
Rocko