If I remove one of the RAID discs and replace it with a raw disc, will the system automatically create another copy? Can this then be used in the crashed unit? or will it expect a 2nd disc to sit alongside it?
The whole point of having a raid1 array is that one of the disks can fail, and the system can still work.
So by putting the two 4.1 disks in the two units, you basically create two degraded raid1 arrays, which is fine. (BTW, if you have done that, you can't revert easily. The disks will 'remember' the array was degraded, and the array will have to be resynced)
The default action when you add a 2nd disk is to resync the array, but I guess you can remove the volume and create a new, not raid1, to prevent that.
If you have the possibility to test the 3.3 disk, and it appears to be healthy and only corrupted, you can try to reinstall the firmware