ILR - Absence while employed in UK

A question for people who have their own companies here.

I have yet to apply for my ILR on the 20th of April, but I have an HSMP until august. I have my own company here and have been doing contract work for some time now. There is a good opportunity in the middle east , a contract of 10 - 12 months. I might be required to stay there for long periods of time (3+ months) before returning to the UK. How will this affect my ILR application ? I will ofcourse be paying Tax and national insurance.

Appreciate any help - thanks.