Great work Yuki,
Yes, the scent of peppermint is lost a little bit, everytime the lid is removed. Some of the volatile oils (VOs) escape easily into the air. I also feel that some of them simply become less potent over time. So the honey mellows, still containing lots of useful constituents from the peppermint, but less of the VOs.
Elixirs: Yes, some bubble more than others. Rosehips is a favourite. I hope it works out well!
Lozenges: If mine are still sticky, I pour more powder into the storage tin and toss the lozenges around in it. When we but lozenges, often they have surplus sugar over them for the same purpose. So I suggest adding more ginger to the tin. See if that helps. Sounds like they could combine happily with more powder.