“Items downloaded from Flickr that have not been imported will be moved to the Aperture trash unless you choose to import them”: Did you upload photos to Flickr outside of the Aperture interface? (i.e. before you started using Aperture or via the web browser) If yes, then those photos are the ones that get synced back to the web section in Aperture but don’t get automatically imported into a project. Once you delete your Flickr account in Aperture, those photos will still be on Flickr but will be in the Aperture trash. If Flickr is the only place they exist, you should do the import first in Aperture to get them in a Project.

As for deleting albums, you won’t lose any photos. Albums do not contain actual photos - only links to photos in projects. When you delete an album you only lose the links. The photos will still be contained in their respective projects. But as I said in the first paragraph, if the photos on Flickr didn’t originate in Aperture, they are not in any project and deleting the Flickr album will move the photos to the trash.

Even if you do remove your Flickr account from Aperture and accidentally lost a photo, remember that they will still be on Flickr and you could get them back via the web interface to Flickr.