Hi Jayk18, You definitely have an interesting story. The Invisalign Orthodontic treatment simulation is designed to move sequentially from aligner tray to aligner tray with the attachments in mind. If the desired tooth movement for that specific Invisalign Orthodontic tray is not achieved (like trays 4,5,6), then those specific movements may or may not have been achieved. I can't speak on behalf of another case since I don't know the specifics, but ideally, those 'bubbles' , 'buttons', 'attachments' should be filled when your Invisalign Orthodontic tray has a void for them.
Invisalign Orthodontic treatment is a journey and usually never finishes in 1 set of Invisalign trays. You will likely have the opportunity at 1, 2 or 3 case refinements and/or a mid-course correction to fix any problems that come along. Almost all Invisalign Orthodontists use multiple sets of Invisalign to achieve the desired orthodontic outcome. Good luck with your treatment!