I can't find a lot of information about the fee waiver, so if it is not eligible they will likely return your petition documents to you with a note that payment is needed. It's technically a denial, but one that can be fixed rather quickly by sending the correct documents/payment. If you do end up refiling, be sure to include G-1145 form that will allow you to receive text/email notifications about your case, and also try to send it through a postal service that includes tracking if you can. That way you can see when it arrives and have one less thing to worry about.
It could also be that the fee waiver will be accepted and the petition will move forward as normal, that would certainly be the best (and lead to the quickest) outcome!
I didn't think the I-129F was eligible for the fee waiver, but I could be wrong about that. Either way you should hear back from USCIS within 30 days, though it is usually less time than that. I would say that average waiting time now is about 2-3 weeks to receive a paper NOA1, maybe 1-2 weeks to receive a text/email notification if you filled out the G-1145 that Georgia16 mentioned above.
