Just look on page 6 of the EEA4 application
guidance notes:
"For your residence in the United Kingdom to be considered continuous, you should not be absent from the United Kingdom for more than six months each year. Longer absences for compulsory military service will not affect your residence. Additionally, a single absence of a maximum of 12 months for important reasons such as pregnancy, child birth, serious illness, study, vocational training or posting overseas will not affect your residence."
ILR falls under domestic Immigration Rules, and PR falls under EEA Regulations. EEA4 is the name of the form to apply for PR. You need only concern yourself with PR as ILR doesn't apply to you in your case. Once you are PR, wait 1 year and you can apply for British citizenship.