After all the mucking about, once the new flash chips arrived it was a bit of a non-event.
What I did discover was that I probably stuffed up reflashing. I'd loaded the flash image, then erased the chip,read the chip to check it was empty, wrote the image and then verified. Which all appeared to go ok. I did the same procedure today but noticed that the write went far too quickly. When I checked the buffer was empty: the read after erase fills the buffer with the contents of the erased chip.
So the correct procedure is erase, read chip, blank check, load file, write, verify.
I'd basically resoldered a blank eeprom. Ooops.
This time I had a positive result soon as I hooked up to the D2. I was able to download the existing map, although it failed on first attempt. When I tried to upload the Td5Alive map it failed at 30%, and I was thinking that I'd be back at the soldering iron. Fortunately I think LR are smarter than Colin gives credit for, as the boot sectors are deleted only after the main body of the upload completes.
The "please wait" with 10% to go appears to be the sector of the memory holding the boot loader program being deleted, and an upload failure after this point bricks the ECU.
It finally clicked that I had a fair bit of junk on the card that had been loaded after I did the initial remap to the LR map for an EU2 Auto. The Td5Inside map had been loaded later again, and the issue wasn't power but slow disc access. After quick trip inside to reformat the card and copy the map across the new map loaded up far faster and without any hesitation.
Lesson learned and I'll only be using freshly formatted cards in future.
Off to take the new map for a test.....

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