Time Outside UK one spouse Visa

My wife got her spouse visa in September 2018, she came to UK in October 2018 with my son who already has a British passport.

They stayed here 3 weeks, collected her BRP and went back to her home country, as she works for a Canadian NGO, the project was for 5 years and she is the finance officer, she was there from the start and now the project will end in Aug 2019, they are very keen to keep her on until finish as she is the one who knows everything.

My question is, she will be out of the UK for 9 months, when we apply for FLR, will she have any issues like visa cancelled or be put on the 10 year route even if we meet all the other requirements?

Also will there be any impact on her ILR if she is given the FLR? We don’t plan to apply for citizenship as she can’t have dual nationality and doesn’t want to lose her Indonesian identity or property there.

Please let me know, I’ve read many conflicting and old advice on the forum.

I want to aslo add I went to Indonesia from December 2018 until March 2019 to spend time with my family.

There is no absence limit for a spouse visa holder.