Upvote:17
Repatriation flights are special, and there's nothing normal about them.
LATAM flight 8070, your flight GRU-FRA looks like a normally scheduled flight. I can go to Google Flights and book a seat on it right now (there may be generally applicable regulations about who can fly on it with Germany's travel restrictions, but that's irrelevant to its status as a regular commercial flight). But LATAM flight 9517, from EZE-GRU, is not a regularly scheduled flight and does not appear in public schedules (many airlines use flight numbers 9000 and above for special purpose flights like charters and ferry flights). It doesn't appear to be possible to buy a ticket on this flight through the normal sales channels.
As such, I would not expect the usual processes like confirmation numbers and online checkin to apply. If this is a repatriation flight that has been chartered by a government, control of the passenger list may be managed by the government (or a tour company they've contracted to collect payment and facilitate the process) and not the airline. The process at the airport may be different than usual. In some cases, consular staff are performing functions normally handled by airline employees (see, for instance, these photos of US repatriation flights in South Africa or this video from Nepalβthere are a lot of consular staff operating stations that are not part of a typical check-in process) and may have their own lists of who belongs on the flight.
The fact that they have booked your second flight, as confirmed by the airline, is a good sign that this is not some kind of outright scam. Ultimately, there may just not be a confirmation number for your repatriation flight. As Greg Hewgill notes, getting to the airport early and following the instructions you were given is probably your best bet now.