I used AFP yesterday to hook up my 10.4 iMac G4 800MHz machine to 10.14, so...yeah. Transferred some Stuffit Deluxe .sea archive, appeared to be OK but we were testing other things.
So I'm not going to be able to say I can reproduce it today, but I
did run into that problem before. I think what I was doing was testing OS 8.6 or something to some variant of OS X (mostly likely 10.6...it's been too long) and transferred the file one way, was OK, copied it back and and it came back corrupted. This was all part of testing the
10.5 AppleFileServer.app downgrade in later OSs that I did 4 years ago, because I wanted to figure how high I could go in OS version before it wouldn't work. (I stopped at 10.10 because that was the newest distribution at the time.)
Both Disk Copy 6 and 4.2 disk images keep the image data in the data fork. The resource fork is irrelevant, that only holds the type/creator info, some other irrelevant stuff and the disk image icon. If you restore the type/creator info using something like: DiskTop (pretty handy tool sometimes), ResEdit, Finder Info 1.1.1, Creator Changer, or whatever, it'll be back to working. The Working with Disk Images section of the Guide has a reference section in case you need to look those up.
EDIT: I only messed with Windows 2000 Server with the Services for Macintosh package installed. When you install the SFM package, some alterations are made to make the system "Aware" of resource fork type files and you shouldn't have problems with them. Windows 2000 does run NTFS the last time I checked, I could be seriously mistaken but I'm pretty sure you can't install it on a FAT32 volume -- if my memory serves me right Win 98SE was the last one to work off a FAT32 volume.
EDIT2: The disk image writing tools I used for Windows are
NOT capable of working with DC 4.2 images. If you are a devout Windows user, I would just use a Linux VM with Netatalk 2.1.6 file server and a command line process for $ dd to cook those up.