Even those who can work from anywhere may still stick to Tokyo so their kids can go to school there...
If they want to return some population to backwoods country, they might also need to move schools and hospitals. It's like a catch-22
The easiest way is probably to keep Tokyo for a commercial hub, and establish a new capital somewhere else, just like Ottawa to Toronto, Canberra to Sydney, etc.
I think they were actually contemplating moving the capital to a northern small city. I don't think it's happening anytime soon but it would help revitalize the north of the country to some extent.