Thank you very much for the advice.
Let's say A, an EU national came to the UK in 2004. Her child B came to the UK and lived with her. A worked during her five years in the UK and achieved PR in 2009. Child B also achieved PR at the same time. Neither A nor B applied for any residence documentation because they were not obliged to. A retired and left the UK in 2010, and moved to a third country. Having been away for more than 2 years, A's PR lapsed in 2012. B, now an adult, traveled extensively but was not outside the UK for more than 2 years. B's PR still stands even though A's had lapsed.
I think my circumstances are quite similar to your example. My family (mum, dad, sister and me) moved to the UK from the Netherlands in 1986. My father was invited to the UK to work for an inter-governmental organisation (ECMWF) for 23 years until his retirement, so would have achieved his PR in 1991, as would I. Neither my father or I have applied for PR before because there was no need for it. My father retired in 2009 and left the UK and moved to Turkey. His PR would have lapsed in 2011, but mine should still be intact because I have never left the country for more than 2 years and my PR status remains independent from my father's status.
Is this correct? Should I write the above story in the cover letter to explain my circumstances?
When did your father move to Turkey? When exactly did he leave? Has he visited the UK since leaving? If so how often? Does he have any ties to the UK?
He moved to Turkey 3 years ago (May 2009). He has visited the UK on an average of 2x a year since then, he still has a UK bank account and his pension comes from the UK. He is able to provide a bank statement as evidence of this.
In the original application I did not include my father's passport (I provided a photocopy of it) as he now lives in Turkey where he is required to keep his passport with him. They did not mention it when they returned the documents to us. In your experience, do you think it could still become a problem?