Thanks both for your replies.
I'm thinking of using shift registers to have all my outputs plugged to only one MEGA, and have a second MEGA just for when the first one fails, or needs an update. Chained Registers are easy to plug to another board, maybe I could even use a series of switches to choose which MEGA is live... Then I still have to move the 50 inputs in an easy way from one board to another. What kind of hardware is used for that ? A big breadboard with jumpers that are attached 10 by 10 or so ?
Would you say this is redundant enough ? If I have to wire it all a second time in the old way, I'll just stop here...