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In law, there should be no ill effect. You are arguing that you have already acquired PR; if, as it seems, your argument is correct, then your rights under EEA law no longer depend on your wife. Now, your position under the withdrawal agreement does seem to depend on your wife: according to the statement of intent, it does not depend on her.
As far as I can make out from the draft withdrawal agreement, your right to be treated under the free movement directive (2004/EC/38) after the UK leaves the EU depends on your still being a family member of your wife. However, the Home Office has announced the rules it intends to use, and under these it will be enough to have been her family member for five years.
Yes, that is correct.
If they do not acknowledge that you have PR, then while you both live in the UK and are not divorced, you will be the family member of an EU citizen with permanent residence; you will retain the right to reside and work in the UK. In 2019 you will be able to and, in practice, need to apply for settled status under the rules of the "statement of intent". She will also need to apply for settled status, though she can wait longer. The child will also need to apply for settled status.
I am no expert on how the court works. Her PR plus the letter saying when she acquired PR should be very useful and her P60s stop the HO claiming her DCPR was issued in error. You will also need evidence that you were resident for a period of 5 years between the marriage and the date of application. Is your marriage certificate a British marriage certificate? Has it already been submitted in evidence?
No.My question is was I overstayed before I got RC in 2014 even though I married and applied RC in my legal status in 2012 ?
If you meet the requirements you can apply. You should ask your British citizenship questions in the British citizenship sub forum please.Can I apply now citizenship or i need to complete 10 years legal process of good character ?