[Terr_]

Perhaps some kind of "SD-card multiplexer" arduino project, where you have 50 SD breakout boards all mounted in a tall stack, each with an LED, and maybe a "reset" button if it doesn't detect ejections. Some circuitry in the middle would set each LED status color, and switch which of the 50 is currently connected to a single set of access pins.

It still involves annoying work by humans, but it would be much more straightforward: See a bay that is showing the "idle" color, remove any finished card and put it in the finished-box, grab a card from the to-do box and put it in, then press the button to signal a new card is waiting.

If that process took 6 seconds, 1000 cards would mean 100 minutes of tedious work, but you can spread it over multiple people or (since the card-read takes time) do it in short bursts interspersed with other activities.