You're right IFW.
Most of them (I'm thinking to the various laser hole protections) can't be written back to real floppies.
However some protections are not so tough... and I was able to copy them even years ago with Project D (Omnicopy). I was also able to copy many Atari ST originals owned by a friend of mine
. (Amiga rules!)
The IBM Assistant series (Writing/Filing/Reporting) is among these.
I wasn't able to copy them with my PC, but I was able to copy them with my Amiga.
Now that PowerCopy Professional has been 100% cracked by StingRay I can archive those IBM floppies... but I would prefer if there was a standard format for protected PC floppy images... something which could be used in emulators and/or, if needed, written back to real floppies by using a hardware interface like KryoFlux.
Will PC emulators support the .ipf format someday?
(DOSBox is absolutely beautiful, but AFAIK it's limited to normal/regular floppy images.)