Is it ok to leave Japan temporarily while change of residence status is being approved?

Currently a student in Tokyo, on a student visa.
Me and my wife plan to apply for spouse visa very soon, but we have a trip together out of the country next month.
Have left Japan during my student visa plenty of times, just fill out the re-entry form at the airport, but does it work the same way if a change of residence status is being processed?

by futurefrom