When I clicked Cancel, another window popped up with a list of the tracks that would be aborted along with another option to cancel and a spinning circle. Since I wasn't sure what it was doing at that point, I waited awhile before clicking cancel again.
Now there are a lot of empty folders on the SD card with the album titles but no tracks in them. I am fairly certain that those folders had files in them that were synced and it deleted them. When I started the sync again, it started from artists beginning with "B" when I had got all the way up to "K" before I canceled.
I'm not blaming you at all psychoadept, you said it "shouldn't delete" the tracks, which was hardly definitive, and I realized I was clicking cancel at my own risk. Well, at least I am now upgraded to version 3.1 while I sync again. It's not a big deal, really.