I think having a limit of 3 (within a timer) to succeed wouldn't be so bad. Add some light-up circles, some nice ascending tones and a bit of animation/particles and it becomes something satisfying for the player to look forward to at level's end. As for exploiting the system to manipulate 3 blocks through in this way, well it may not be the developer intended solution and you'd have to design a liiittle to avoid cheesing, but if the player can really get three correct blocks through in this manner, then that'd be just another creative way of winning, eh? And probably pretty satisfying to pull off, or even for you to see.
However, speaking more grounded, I think if a player edits something in the machine while it's running, all the current blocks should simply *poof!* But it keeps running. An easy solution that solves your problem.
Drop a link to your Discord and I'll lurk in there, but truthfully I'm too busy with my own dev projects to hang out on Discord much these days, fair warning :)