Ahhh, OK, found the trouble. One of the two books - which shall remain nameless - has a css file which is 112 kBytes! There are over 7700 lines which all look like this:
#cfs_2121 {
font-size: 83.333333%
}
Only the label changes! Somebody's conversion software sucks, big time!
And the Kobo scans the files to insert them into its database... No wonder it was taking so long!
Got rid of that file, and all is well
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