Hi,
I assume that you are plugging the MFM card into the PC and trying to read the HDD. I suppose you would have to, the MFM drive would not be able to be connected to the IDE interface.
Of course, MFM needs two (smaller) flat ribbon cables and IDE needs only a single but wider one. Only the power supply cable is the same.
If you are using an assembler routine or something similar to call bios/dos IRQ's to read hdd, remember that if it is a non-dos partition, even the bios will probably not see it, bios is designed for dos/windows use.
Yes, that's also true and approved by my experiments

the HDD content/partition is not recognized by DOS respectively the BIOS.
I programmed the controller directly by accessing the corresponding hardware ports without any BIOS or Interrupt calls.
Just to keep you informed, here is my workaround:

Coincidentally I got in touch (via EBay) with someone who sold me some spare parts and a few software disks for my robot. Unfortunately the Utility disk was of Version 10.1 (not the needed 8.2) and didn't work correctly with my V/V+ 8.2 system. But having the Utility programs on diskette for the first time, I was able to "patch" the file copy utility (Ver.10.1) with a diskeditor and use this patched version to make me copies of my wanted Utilities subdirectory (from HDD to floppy).
Puuuuh, sounds complicated but it worked.

Now that I had backups of the complete system and could install a new winchester drive and re-install the whole software.
Thx again for you commitment
greetz
addi