Best practice for managing Covid vaccination documentation

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Is there a way to transcribe all three shots into a single document? Ideally with a QR code and without anything hand written?

There is no way to do that with the EU Digital covid certificate system. The QR code only encodes the last relevant “event” (test or injection). For vaccination, there is also a field for the order-in-a-series of vaccines (with values like "1/1" for the Johnson & Johnson/Janssen vaccine, and "1/2" or "2/2" for Pfizer Comirnaty or Moderna Spikevax) but no other details on the earlier injections. So whatever else you do, if you need to rely on an EU certificate, you need to get your last booster encoded in a way that's accepted by the verification app you're interested in.

In most countries, the verification app only looks at the last relevant QR code (depending on the rules in place at that moment, it can be a vaccine or booster shot, a recent negative test, or an older positive test) and displays a go/no-go decision with minimal info. The whole system was designed to make it possible to make a decision by scanning the QR code without looking at anything else. That QR code can also be printed on paper or stored as a picture without using any specific app.

If someone wants to get more information or examine the whole series of injections, as you experienced in Germany, then they need to look at several QR codes or documents. Because that's how the system works, it makes sense to provide two QR codes in your situation and it is in any case impossible to provide a single QR code with all the info.

I am aware of many other annoying cases (people who had to switch vaccines based on availability or changing recommendations, people with atypical vaccine sequences because they caught Covid at some point) but that's not really a problem that can be fixed by the certificate issuer. As the validation logic is in the app and different countries use slightly different rules, it's entirely possible to get an EU Digital covid certifcate and yet be unable to enter somewhere. It's also possible for your last QR code to be recognised in another place than Germany.

I have no idea about the US side of things.

What's currently the most "usable" form of vaccination documentation for travel?

For international travel, things are different, nothing works with QR codes. Even if you have a “simple” vaccination course (say three Pfizer Comirnaty injections) fully documented with EU QR codes, airlines and border guards still want to see human readable descriptions of these injections. If what you have is the typical EU Digital Covid certificate print-out, airport staff will not scan the QR code but ask to read the other side. I have experienced that multiple times both inside and outside the EU.

So the best documentation is either a PDF or printed proof of vaccination (with dates, description of the vaccine, stamps, and signatures) for each injection.

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