I accidentally removed the hidden modules added to the crystallizer with an inserter by having the inserter take from the last row from top, second column from left with the pipe input facing topward and the inserter situated one block left of the bottom left part of the crystallizer.

You're not supposed to do that. Put it back!

As for the actual fix, 0.17 is adding "no-inserter-pickup" and "no-inserter-dropoff" flags that I'll add to the beacons. I don't think I can prevent this in the current version, since the beacon's hitbox needs to be the same size as the crystallizer so that it's powered if the crystallizer is. Which also won't be necessary in 0.17, since it's adding an "energy source" that lets things run without being powered.

I think I'll add a "refresh" console command so you can at least easily put things back to how they're supposed to be.