Those of you who are doing Invisalign with missing tooth/teeth, does your trays cover the socket?

Bit of a weird question, but previously I got up to Aligner 3 until I had to do a rescan due poor fit and the trays didn't cover my full set of bottom teeth where I have my missing first molar, so it stopped at the gap and my socket and last molar wasn't covered :') but with my new set of trays from rescan they are and now I have to start over with the tray set 1. This is a nightmare but I'm wondering why now my sockets are completely covering my socket cause it feels weird without a tooth actually being there to cover!