In a situation where a fee was disclosed on a GFE (for example, a survey) and it turned out that the service was not needed (an affadavit was sufficent) does the survey fee still show on the HUD for purposes of determining if the actual fees were within tolerance? Or must the survey fee be left off the HUD entirely?

No, you won't show it. See the last (or next to last)HUD newsletter which covers how to handle this situation.

Our bank sells to an investor that is disregarding the RESPA Round Up Q&A and is still requiring our bank to list the GFE fee on the HUD comparison page even when the fee isn't charged. (I called them to point out the new information and they basically said "we don't care, do it our way or we won't buy your loans!) What do we do?

You need to find out how your examiner is going to examine the documents, according to Appendix A or the Round Up. If the Round Up then you best be finding a new investor.