@ixtba: Got it, thanks! I certainly had some time to look at the pretty status bar when doing a ~150 collections import
The second import went fine btw, nothing blew up ^^. I'll just have to tweak the calibre plugin to disregard the current collections.json file and history, since, unless you do an export each time you intend to refresh the collections through Calibre, it risks being not in sync with the the actual CC db, so you end up possibly loosing items in Kindle-only collections (in my case a Reading/TBR collection that's managed entirely from the Kindle).
(Am I right to assume that it can delete *items* from an existing collection during import?)