ILR for wife, passport expires soon

My partner has been on spouse visa in uk i am british citizen.

After the initial 2 year period was up we applied for FLR as life in uk test had not been completed. Due to unforseen circumstances ILR was not applied for on time and partner returned to home country before re-applying for settlement visa again. You still with me i know its a bit of a long one but the questions i have now are

As mrs has been in uk since Nov 2005 on original settlement visa and FLR, does that still qualify for 2 year period? Or the fact that she has returned to home country old visa expired and reapplied for new visa and returned back to uk mean that she has to wait for the 2 year period from this visa? She has been out of the uk since 1 Nov 2009 and returned today.

How many days of remaining out of the country is allowed?

Any help would be appreciated.

Thanks

See also Time spent outside the UK.

Perhaps she could argue that her probationary period had started on her initial entry of her first spouse visa. KOL will be required for a settlement application.