Need to stay more than 90+ days due to family emergency. Will it affect my PR application in future?

Hello everyone.
I have been to my home country since December 27 2023. And our scheduled flight to Japan is on March 24 (coming Sunday) 2024.
It will be about 89 days.
I planned this trip not to spend more than 90 days as i heard many rumors it might affect future PR application.

But suddenly my wife’s health is getting poor. The main reason coming to my homeland is also for my wife’s operation (gallbladder inflammation) .
She had an operation about 2 months ago and was perfectly fine. But last week, she had same kind of panic attack , and today too.
Our flight is day on two days. We also have 5 months old daughter.

Now I am afraid, if I extend my stay here for about 15-20 days, will it affect my PR application in future? As I will be eligible to apply for PR in coming October (10 years route).

Also I am not on holiday or paid holiday. I have been working remotely according to our japanese/company calendars and schedule. Company have no issue wherever I work from, as long as I complete the assigned tasks and presence.
Tax, insurance, pension are automatically deducted via my salary every month.
Our apartment is still there (rent paid every month via bank account)

I am on humanity/engineer visa. (Expires on 2025 nov) My wife and daughter in mine dependent visa. (Non Japanese).

by Run_the_show

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