OK, I rebooted after filling drive E: (12GB) to .98GB free and G: (6GB) to 225MB free.
Upon rebooting, I found that the red alert two folder I'd put on (and run from) drive G: had gone, and a zero byte "found.000" folder had appeared. The other two (>2GB) files I'd put on were still there. Chkdsk found no errors on that partition.
Chkdsk found various errors on the E: partition, but recovered them successfully it seems.
I'm copying RA2 back to the G: drive (this is, after all, a drive I don't use because it IS FAILING.) I am then going to try to extract the rar archive to see if it's OK, then reboot and check the disks again.
So far I'm not sure whether these instabilities are down to the instability of the "mod" or the logic errors the disk controller has experienced (though since the mod I've not noticed any evidence of the sounds I've been having previously, which is rather strange.)
I'll keep you posted.