But something resets the floppy emulator when exiting from direct access(your manager). It`s only to me?
What you call as reset? "Reading FAT", etc? It is a normal.
Burning EPROMS is something always has intetested me, but seems complicate, doesn`t it?
No, it is a very simple, especially with the modern programmers (the sw know all parameters more than 1000 IC types).
Only complication the erase: need a UV lamp to do it. I have a germicidal tube which are looking a neon tube. I used a normal neon sockets and ignition switch for build EPROM eraser, putted all in a home made closed box (UV light dangerous for the eye!).
Todays FLASH ROM ICs (29xxx and 49xxx series) and a older EEPROMs (28xxx series) are electronically erasable, more comfortable than the old EPROMs (27xxx series)!
The FLASH ROMs use only single 5V supply for the erase/programming, then it is can be used in the Enterprise system!
I already do it 
For the MX/AMD 29F0xx series I wrote programming routine.
If soldering few wires not a problem for you then adding FLASH ROM chip to your card are the easy way to test ROM programs.