Letter voting can be applied for, you get the vote and have to give them your id number (or passport no) in the application - that way - and because you can only apply in one place (I think, haven;t tried it yet - but you can only ever be registered in one place in Germany - you have to give your previous address and they automatically forward your information to the new place.) they can check if you have voted in person, because they cross you off by hand, when you get your voting paper.
So, unique identifier, paper and volunteers for counting. simple enough.
The other thing, For me technology is always the slave and never a necessity. If something can be done without technology, simplify. Never use technology for technologies sake. but that is just me.