It would be OK to confine him. (and I don't blame you for wanting to do it either). As a matter of fact, when the problem is behavioral (vs. medical) confining to one room for retraining is part of the process. He will be fine, and you will probably not have to do it for long since the problem was medical. Once he feels better he will make it to the box again.

And questions, even 1000 of them, are not annoying, especially when you just want to learn from other people's experiences. OK?