If lose residence status in Japan

Hi all,
Please ignore my previous question that got posted mistakenly before it was completed.
Hopefully I'm not the first person to have ever encountered this problem.
My family (wife and 1-year old son) was living with me in Japan with dependent residence status and left Japan last year with special re-entry permission. But due to Covid 19 and no flight to Japan, I'm afraid that they may lose their residence status although their residence cards are valid for another 2 years. So as a rule, I need to process everything from scratch that I did for them to enter Japan 3 years before. I have the following questions:

Should I inform the City Office about this matter, before they lose their residence status?
If they lose their residence status, what will happen to the benefits I am getting in terms of taxes and child rearing allowances?

Sorry for my bad English.
Thanks in advance!

Should I inform the City Office about this matter, before they lose their residence status?
You should inform/talk with immigration office. They are the one handling resident status, re-entry etc.
http://www.moj.go.jp/EN/nyuukokukanri/kouhou/m_nyuukokukanri01_00003.h... (Note2)
Check with immigration with regards to your above mentioned problem.

The special re-entry is for 1 year period, so if they can re-enter before the 1 year period, no problem.

So you are Japanese, and your non-Japanese wife and son have been living in Japan with you on “dependent” status, but now they are staying temporarily outside Japan, and cannot get back into Japan before their resident status expires.

I have looked into this on behalf of a friend who is in a similar situation, and as far as I can tell, if it expires while they are outside Japan, you (the sponsor) will need to go through the Certificate of Eligibility process once again, BUT considering the situation, you need to submit only the (1) application form and (2) reason statement (“unable to return due to COVID-19”). You do not need to apply with all the other documentation, which you’d have had to 3 years ago.

It is mentioned here
http://www.moj.go.jp/nyuukokukanri/kouhou/nyuukokukanri01_00155.html?f...

If you want to read it in Japanese, click on the link with the following phrase on that page:
帰国困難者及び在留資格認定証明書交付申請の取扱い［PDF］（2020.2.28）
Which should take you to:
http://www.moj.go.jp/content/001315948.pdf

If you want to read the English, scroll down and click on the link that says:
（英語・English）Handling of residence applications due to the spread of the COVID 19 disease［PDF］

And it is under 2-(iii).

In the case of “dependent,” the sponsoring Japanese spouse would be the one who writes the reason statement.

I am not familiar with the taxes and allowance issue. Considering the extraordinary circumstances, I hope they allow for special cases…

Thank you so much for the helpful suggestions. You released most of my tensions. 
So my family will have to issue the VISA only by submitting the CoE at Japanese Embassy to enter Japan? 

To be clear 'dependent' visa/statuss is for non-Japanese spouse and 'spouse' visa/status is for Japanese spouse.

In OP case, when OP said 'dependent resident status' , that show that OP is not Japanese ?

As mentioned before special re-entry permit is for 1 year period, so if your wife and son can re-enter within that 1 year period, they won't lose their resident status. Due to Covid-19 situation, immigration may give some exception BUT depending on when your wife/son depart out from Japan. So check with immigration.

So my family will have to issue the VISA only by submitting the CoE at Japanese Embassy to enter Japan? Yes.
If so happen your wife/son resident status is cancel, you will need to apply for COE again with immiration in Japan and submit the COE at Japanese embassy. That is starting applying for COE-Visa again like before.

Whoops, I got the “spouse” and “dependent” status mixed up. Sorry. So the OP is not Japanese.

OK, it is about the last part mentioned in the post above by @.. (guest), there is special handling for application of CoE for those unable to return due to COVID19.

Usually, to apply for CoE for your spouse and child, the sponsoring family member would have to submit the application form (filled out), along with a lot of documentation showing the relationship, income, etc.
However, this time, if their status expires while they are outside Japan and they are unable to return to Japan due to COVID-19, you only need to submit the (1) application form and (2) reason statement (why they could not return). You go through the simpler version of obtaining CoE.

Oh! I am so sorry for forgetting to mention that I am a non-Japanese. They left Japan on 1st September and were supposed to return by January. They avoided travelling in Jan-Feb and now have no flight and entry ban. 
So I understand now, how they can enter Japan if they lose their residence status. Thanks to everyone for the helpful suggestions. They probably get a new residence card if they arrive at the Haneda Airport with a new COE and a new VISA. Any suggestions about the pension book, my number card, and medical card if they lose the residence status? All will be new again?