The plugin wouldn't have erased your collections on the Kindle anyway in this situation. If you did a Create with a blank column, it would have left all the collections as Kindle only (unless you unchecked that box). And there is always the restore collections from the last create/edit. But I can understand your concern
I'll test out editing/importing. Technically it shouldn't make any difference, but that's what bugs are
Yep, best to edit directly in Calibre and run Create. Edit was mainly added for people who didn't use or want to use Calibre to organize their collections, although it should still work fine. Appreciate the feedback. Hopefully I can figure out what the issue is - and at the very least I should be able to add a check that the plugin has actually read collections from the Kindle before proceeding with the import.