I don't understand why selecting configuration files with the side tube is an issue. You've had a quadstick over six years. You've made dozens of configuration spreadsheets and downloaded them to your quadstick. This has to be some kind of misunderstanding.
When the quadstick connects to the PC and the PC prompts you for the default behavior, the correct answer is to "take no action". Do nothing. Seeing that prompt is telling you the you did in fact select the correct configuration file since the Quadstick is switching from a pure XBox 360 game controller mode, which has no flash drive, to a USB mode that does have a flash drive, which will allow you to manage the quadstick using QMP.
You went in there (wherever there is) and cleaned out some files.... Yikes. The quadstick configuration is contained in files that need to be there. Hopefully the needed files are still there.
Whatever you do, do not remove the default.csv or prefs.cscv.
If you start QMP, go to the Games tab and click on the Print file list button, a browser window should open up with a window you can print that has the instructions for selecting the files along with the pattern of flashing lights for each file.