Child’s Irish passport application

Hi there, My name is Ahmed i need advice regarding my child’s passport application.. I am having issues with DFA regarding my child’s passport.. I wil give brief introduction about myself i am legal in the country since 2005 and i hold Stamp 4 EU-Fam from 2012 to 2017 I have 2 children from same marriage.. Department of justice revoked my visa in September 2017 reason for that is my wife was not exercising her EU treaty rights..
Note:- Me and my wife we were living separate from June 2015 - March 2018 she was on single parent benefit but we always had good relation i looked after my wife and new born daughter during that time.. In 2017 september I applied on my Irish childs behalf and i got stamp 4 since then to this date..
In April 2018 Immigration visited my house and they checked passports of my wife & daughter and mine GNIB card and passport since then i had no interaction with department of justice
My second child was born in may 2019 and I applied for his passport submitted all my documents including Letter confirming they revoked my visa.. They said they will not be able to issue my childs passport as my visa was revoked and requested to send my wife’s documents for last 5 years and i did 4 weeks later when my wife called DFA to status of application one of the officers dealing with the application called back later and apologised saying they have SHRED all the original documents for last 5 years and requested us to resubmit all those documents again we manage to gather not all but some of the documents confirming my wife was in the state still they are saying they are not satisfied and they will need to contact Department of Justice for more clarification on my visa status..
I don’t understand where to go and what to do from here
Your advice will be much appreciated

what is the nationality of your wife and how long has she been living here ? if she is an EU citizen and has been living here for more than three years then you can apply on her behalf.