It may be much easier to avoid troubleshooting. A quick way to get it back up and running is create an image of the good SD card, and restore that image to the bad one

That is probably the best way. I will need to sort out hostnames etc but that is pretty trivial.

Double, triple and quadruple check that you've got the right disk, or you could very easily and quickly hose your system

Everything I have written, including the crontab entries are backed up safely - but yes, I shall take great care with which disk is which :)

I don't have a Linux box to do this on but Win32 Disk Imager should do the trick just as well thanks.