EEA (FM) requesting passport back

[jackman1]

Hi I have a two part question.
I am an Australian and my wife is Czech. We got married in the UK and applied in Czech to have her name changed (due to new passport and id card required/not out of date) which should have taken place by now but hasn't. Importance of this is because once they process the request her passport becomes invalid within 3 months and we now need to send all documents in for my EEAFM application

1) do we send all the documents in now even though there is a strong possibility her passport in 3 months time will be invalid or do we wait?

2) I travel for work and really need my passport. How long does it take to get back if I request it and will it affect my application? Thanks