About Certificate of Alien Registration

I am the child of my biological mother and married to a Japanese(my current step father) and officially adopted by my step father on 2006 (9years old at the moment) .I was holding a certificate of alien registration but unable to renew the certificate(confirmation) after I reached 16 years old since I went back to the Philippines on 2012 (the year when I become 16), a year after the earthquake happened on 2011, since then 11 years have passed and I am 27 years old now. Am I still eligible to apply for a resident visa?

Anyone can apply for a visa if they meet the requirements that is needed for the type of visa.

ARC or alien/gaijin card was replaced in 2012 to resident card@zairyu card.

What resident status was it you had then ? Long term resident ?
Your adopted step-father did not apply for naturalization(acquire Japanese nationality) when you were still residing in Japan, so you are not Japanese citizen.

If you want to use the adoption for visa application(long term resident), it is only for child upto 18years old.
https://kekkonvisa-nextstep.com/nihonjinnohaigusha/youshi_en/
https://www.tn-office.jp/15520175743139

So only way is a working visa.