Track them, dagnab it.
List questions in a spreadsheet and assign a unique identifier to each.
Annotate the master copy of the RFP with those identifiers so you know something is outstanding about that aspect of the requirement, whether it’s the SOW, draft contract, response instructions, or evaluation criteria.
Update the spreadsheet when the answers come rolling in.
Comment the master copy of the RFP with the answer, especially if the client doesn’t issue an amended RFP.
And if you’re thinking that this sounds like a lot of work, well, it can be. So assign someone to be responsible for it.