I suppose I viewed the DX5 as the independent radio transmitter that it apparently is, according to Phoenix RC, in that the DX5 can be unplugged from Phoenix RC sim and used to control real RC aircraft, or another RC sim, maybe. I bought my Reflex XTR package quite a while back, but I do remember that program would not work without that red USB-to-transmitter dongle supplied with the CD. What I don't remember at all, though, is whether Reflex XTR was shipped to me with its own transmitter, or whether it just arrived with the USB dongle, and a list of compatible transmitters.
On the assumption that Reflex XTR would work with a number of popular transmitters including the DX5 that came with Phoenix RC, provided that the Reflex USB dongle was used to connect with the transmitter, I may just have bumbled my way towards a disaster for my DX5 transmitter, though I still hold out hope that the axis assignments might have been muddled and maybe just need re-setting.
I'll try new batteries as well, just in case they were running low enough to make the transmitter give off those rapid beeps and shut down. If those fixes don't work, I expect to engage in some wailing and gnashing of teeth, as the possible damage sinks in and my grandpa's old saying comes to mind " If it ain't broke, then don't fix it."