I tried again later and this time all the Questionable ones were gone. So I guess “Fix all” really did work quite quickly, at least on my broadband.

One setting I changed on the second run was to remove the check for duplicates. I do use the Bookmarks toolbar and find it quite handy for places I visit frequently, and leave a copy in the main bookmarks menu in case one or the other gets corrupted. And naturally, CheckPlaces insisted on “warning” me about the (deliberate) duplicates.

(Edit) Apologies to those who feel we wandered too far off the main topic with this sub-discussion. I for one am satisfied with the result and done with it.