I agree that he should get confirmation, in writing, that the 2IC is ordering this change and accepts that:
* It will take X time per user account,
* May break things (risk assess it),
* Will not be able to be interrupted during the process, so all other jobs to be on hold,
* He will accept responsibility for any down time or unintended consequences of this (pointless and stupid) change.
Ensure that, in the confirmation, he makes clear his reluctance to do it and belief that the risks outweigh the "benefits".
Then he should get on with the job. His arse is covered in case of problems, but if the boss tells you to do something, you either do it or look for work elsewhere.