Apps are not the solution. Invariably, they will be hacked or "amended" at some point.
It is not true that when counting lots of votes you lose track. Broken up into boxes or whatever, you count one box or bundle at a time, put the results on your tally sheet or ledger for that box, SEAL the box, then go on to the next. If you count up the box tallies, you're not trying to keep track of hundreds of thousands of votes.
One person from each party participates in the ballot counting. One or two observers from each party sign off on the count of each box.
Watermark or otherwise insure the paper ballot is genuine.
The first thing that must happen is counting is done at the polls and records kept of the polls count transmitted to state election offices. Without oversight of what the state posts vs the polls, skullduggery can happen there. People don't check.
Ballots, AFTER counting, are then transported wherever they have to go, under guard.
Foolproof? Nothing ever is. But any electronic/computer system is open to manipulation. The size of the manipulation possible with computer systems is way, way more than hand counting.
There are always advocates for the holy grail of some type of computer voting. The best thing here is the KISS principle. Paper and people and checks and balances.
Watch all the excuses for voting machines- handicapped was one of the first ones. And for the handicapped, yes. But once that door opened, it was machines all the way. They will use any excuse to keep using voting machines that can be hacked.
Oh, and the National Associations of State Election Officials, Secretaries of State, Attorney Generals and the corresponding associations for county officials need to be in the garbage heap.