Indefinite Leave to Remain (ILR), EEA Route... pls help

I am Spencer from Uganda and have been married now for over 6 years. I got married to an Estonian lady in Italy on 12 August 2008 and we were living together there. On April 2011, she (my EEA wife) came to the UK and started working immediately. I the non EEA spouse later joined my wife and kid here in the UK on Feb 1012. I applied for a residence card and I got it on Aug 2012. My wife became pregnant and later on took a leave of absent from her employer and then went to her country (Estonia) on Oct 2012. She then delivered a girl child there and came back to the UK only on Sept 2013 (Approx 11 months). Even as she came back, she has not been working and now she is pregnant again. This time, the pregnancy is so complicated as the doctors here says there is a very high chance of down-syndrome, so she has gone back to Estonia where she might deliver there. So, I want to ask a few questions as follows:
1) She has been on and off from the UK for almost 2 years without working. Will her absence from work affect my application for Indefinite Leave to Remain (ILR) ??
2) Her on and off from the UK, will it affect my application for ILR)??
3) As she has been absent from work for 2 years due to pregnancy, is she still exercising the treaties rights?
4) I have been working, but I don't know if I have lost my rights as a spouse of an EEA citizen.

I seriously wait for an answer so that I can know how to prepare my application, Thanks

It will all depends if the absence can be considered as absence for a reasonable period.

In some case, she will not loose her worker status due to maternity leave.