autoexec.bat stored in an EEPROM

Hi everyone!!

I have this problem with a pick and place machine. The program of the machine is stored in an EEPROM and when i start it up it it goes directly to it's start-up menu.
Now, the machine works with DOS (it loads an autoexec.bat and a config.sys) Can i remove any line that loads the .exe file that starts the machine in order to get the MS-DOS prompt at startup?

Sorry about my english!