Seems to fix it. Here's what I did:
Uninstalled Calibre 0.7.1
Installed the beta and started it
After it got the book list, I deleted a couple of books from the SD card
metadata send took just over a minute
Deleted a book from the main memory
metadata send took just over a minute
Then I came here and saw your post about wanting debug log..
Ran the debug version and added back the book I had deleted from main memory
metadata send took 4 seconds (of course)
Ran the non-debug version and deleted the book again
metadata send took 4 seconds
So I think it works, but you need to 'touch' both main memory and the SD card (and/or the memory stick) to get all the metadata sorted. Then you're good to go.
Huzzah! Thanks!
Now to go back to thinking up clever things to do with custom columns :-)
(edit - fixed typo)
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