Here is the debug log file (after some edit to take out the contents of Calibre and the Kobo) with the automatic metadata update enable. Remember as I said before the series and the collection don't correspond totally. When they are the same the collection content is not modified by Calibre.
I'm sorry to have call the kobo utilities a workaround (english is not my native language) when it is a good substitute to Calibre for some function.
And for a laugh. It takes me 2 hours to rebuild my collections but I forgot the metadata automatic update was on when I plug again my Kobo into Calibre...
