Dear Mark,
Thankyou for your help, I've deleted Java 1.3.1 off my computer - it was left there after downloading a newer version of Limewire and Java 1.4.0 and I didn't know that I could delete it - so that has solved that problem.
I'll be backing up both the 'full' download.dat file, and the 'empty' one that replaces it after a crash before trying the cut/paste thing.. but I'll also be shutting down Limewire more carefully in the future.
Cheers.