Just as an update, I attempted the LhA (and LZX) method of archiving the drive and I encountered a weird problem that I couldn't get around.
Essentially, the process went like this.
1. Create a boot disk with AmiTCP, FTPMount and LhA on.
2. Boot from the floppy and archive DH0: to a file on DH1:
3. Use FTPMount to move the archive to the NAS.
4. Switch out the IDE Drive for the CF card
5. Boot with the floppy and bring down the Archive from the NAS.
6. Decompress the archive.
Everything worked just fine until the decompression stage. At which point, no matter what I tried, LhA and LZX both complained that the Archive was corrupt.
To double check that the FTP process wasn't mauling the archive file, I put the IDE drive back in and downloaded the archive from the NAS to the drive and used the "t" parameter to test the archive. All files were present and "Tested OK". File count 927.
When I tested the archive saved to the CF Card, corruption was reported and only 166 files were in the archive. Very odd indeed.
So after a couple of days of testing, I've plumped for an easy way out. I've bought a 3-way IDE cable so I can plug in the drive and CF Card at the same time, transfer the files that way and then remove the drive. Hopefully that'll work...
I'm really puzzled as to why the LhA and LZX archivers both exhibit the same behaviour when I swap the IDE drive out though. Very odd.