I dumped the ROM off my PDA, but the only format it will dump as was *.bin I have attempted to write it back using the same program but it didn’t allow it.

question.
is the ROM image written to the PDA as it is just one file and the PDA interprets it as an array of files? or does it extract the files ?

The extended ROM might not be accessible but doesn’t mean its not there. in the diag. menu it shows flash 1 and flash 2.

Conclusion
When writing to the PDA the ROM file is first copied to the extended ROM. Then extracted (installed) to the main ROM