Did RFE letter received by mail mention replying online? Just because you can doesn't mean you should. Most likely the instructions in RFE provided address to mail response to. Technically, USCIS doesn't have to take any response provided online if RFE instructions don't mention it. Add to that glitches in USCIS IT systems (duplicate A numbers, missing case statuses, etc etc) nobody can guarantee uploaded evidence won't be silently discarded / lost / agent won't have permission, desire or training to see it.
Sometimes it is OK to follow the suggestions from members who've seen it all. I think @K1visaHopeful is coming from a good place. If I was paid $10 every time I see people's packets being rejected due to declined credit card payment, I'd get a Michelin star dinner for free. Yes, many times USCIS offers something, but it doesn't mean just because it's there it's a good idea to use.
If online RFE reponse is lost and USCIS says you never sent it, how are you going to prove you submitted it? Do you get a confirmation email with some unique receipt number (like AR-11 online)? If not, I'd respond by certified mail / UPS / Fedex with proof of delivery. So that if USCIS claim they never got it, I could argue they received it.