@Celyn455this reminds me of a guest who kept asking for butter knives. I directed them to them and they said they weren't butter knives. I asked them to describe the knife they wanted and they described a steak knife. I directed them to the steak knives and they left private feedback to get some butter knives...
Either your guest was scamming for a refund or there was some legit problem with the toilet that they were not communicating properly. Sometimes low flow toilets have difficulty flushing. If your guest had some digestive issues it may have taken a few flushes to remove waste. This could be something that embarrassed the guest and perhaps they have a different type of toilet at home. Many people would not be comfortable describing their bathroom habits to a host so you have this odd exchange. This explanation is my "benefit of the doubt" possibility.
What is more probable is that the guest created an imaginary issue in order to get a free stay. It sounds like you did everything in your power to fix this problem. My review would be something like the following:
So and so was communicative and we got off to a good start. However I was concerned that they reported an issue with the toilet and asked for a refund. Upon multiple examinations of the problem by both myself and a plumber, the toilet was working properly. We are still puzzled as to what the issue could have been, as we don't want any plumbing concerns for our guests, and worry that so and so did not fully enjoy his time with us due to this hiccup. Otherwise left the place in good order (if true.) We wish so and so the best.