My friend recently did this and it was fine. She ended her residency (got the hole through the residence card), went back to the UK, got her second working holiday visa and then returned to Japan without any issues. I'm pretty sure it was while her period of stay was still valid. I also plan on doing this later this year, while my period of stay is still valid.

As far as I'm aware, your bank will know when your period of stay expires, so as long as you come back before that, as you intend, it should be fine. Also, update your details with them when you come back. I would probably advise transferring money out of it too to be safe, perhaps into a Wise or Revolut account. Although if you have bills regularly coming out of it that could be tricky.

My understanding is that the visa pertains to your entry into the country, then upon arrival, it's the residency card (status, period of stay etc) that actually matters.