After checking again, it seems that you might be able to check in separately and get in the upgrade list then. But you do seem to lose the early upgrade
Why don’t you separate one of your companions from the reservation and link them to yours this way should not mess up the upgrade and still be connected (in case of delays etc)
“ Traveling with two or more companions:
If you and two or more companions are in the same reservation, all Members must have Medallion Status or be a partner airline elite member in order for any Members to be eligible for upgrades. Each Member should check in separately and they will clear for their upgrade at their respective clearance priorities.
If the party is comprised of all Medallion Members and everyone checks in together, then the party will be eligible for upgrades at the lowest tiered Medallion Member's clearance priority.
If there are any General Members in the reservation, and everyone checks in together, no one in the reservation will be eligible for Complimentary Upgrades.”
https://www.delta.com/us/en/skymiles/medallion-program/medallion-upgrades