Also, what are you trying to flash back with? A romimage, an initrd & zimage, or an OSpack?
If initrd & zimage, try also getting the bootflag.txt file from the rootfs toolkit (
https://www.oesf.org/community/66.180.235.230/download.php/10/rootfs_20011119.tgz). Add it to the CF card before you flash. That probably won't fix things given the symptoms, but if that 4-byte file is wrong, lots of things won't work right.
However, it sounds like the updater program is trying to do the wrong thing (like maybe copy stuff off the end of your internal flash), which is probably because it is for the wrong system. Perhaps you can flash down the correct one, but if that hoses it, I don't think there's any saving throws left.
Probably your best be is to get one of the older ROMIMAGE files for the 5000d and try updating to that. They contain the updator program along with all the other executable stuff (diag monitor (collie), boot loader, initrd, zimage, bootflag.txt, and one or two others).