non EEA spouze and dual citizenship

Hi All

I am really confused and not sure what to do next in regards to my wife's status

I moved to UK in 2008 as a EEA citizen with my non EEA wife.
She got family permit issued in February 2009 valid till Feb 2014.
Unfortunately her mom got ill and she spent 20 months in Brazil between Jan 2011 and August 2012.
When her family permit was due to expire she could not apply for PR due to her absence in 2011 and 2012.
She was granted another 5 years family permit Feb 14 to Feb 19.

In the mean time I became British citizen (January 2015)

What do we do next? Apply fo PR? Will my dual citizenship affect her right to get pernament residency?
If yes, can she apply for ILR?

Please advise