The new MIOS bootloader version 1.005 is now available under http://www.ucapps.de/mios32_download.html
It got a "permanent parameter storage" for options which are referenced by (most) applications.
Parameters can be changed in the MIOS Terminal after the "Bootloader Update" application has been uploaded.
-> type "help" in MIOS Terminal after upload
The parameters won't be overwritten by applications, even the next bootloader update (via MIDI) won't overwrite them.