What might be happening is without the .exe that initializes communication with the uCOM on the AV board (due to empty flash disk) the reset watchdog's timer expires and it resets the Navi because it thinks it's stuck.
If you don't have enough time to copy the APL folder from your My Flash Disk backup back over to the flash drive before reset, there might be another option. If you've got Testmode 2.3, there is a file in the "testmode" folder called CopyTool.mscr. It's a script that gets executed by the CopyTool.exe (really Mortscript.exe that's been renamed so the AVIC executes it to enter testmode). You can edit CopyTool.mscr to add instructions to copy at least the APL folder over to your flash disk so that the uCOM init (I think it's called "initucom.exe") command gets executed which will reset the watchdog timer and thus keep you in testmode until reset. Use the XCopy command in your CopyTool.mscr file:
XCopy( source files, target directory [, overwrite?[, subdirs? ] ] )
So I think the command will be (assuming there's an APL folder in the root of your SD card:
XCopy( "\Storage Card\APL", "\My Flash Disk\APL", TRUE, TRUE )
Good luck.