Family Visa Extension

Hi, I need immigration advice, this is for my wife, she come in UK in July 2010 as a student depended, I got the ILR in 2016 and got British citizens in 2018 we have 3 kids born here and all British citizen, my wife throughout my depended visa leave to remain, in 2014 I got business visa and she was my depended, some financial circumstance she travel back home in march 2014 up to November 2015 (almost 20 month) she was valid visa up to December 2016. Because my daughter was ill so she stay back home with her family we have all evidence of this. She come back in 26th November 2015 and her long residence break down because she spend long time in back home, I got ILR in October 2016 same day, Then I apply my wife 10 year route as a partner visa and granted 2.5 year, because I do not fulfil the financial requirement, and our kids got that time British passport as well. Now we got third extension on 10 year route, and finish 30 September 2025, no overstay, no refusal visa in last 14 years,
My question is we starting 10 year route clock again when she enter in UK with valid leave to remain 26 November 2015, now we got 3rd extension, her 10 year finish 26th November 2025 but this extension expire 30th September 2025 , only (57 days gap)
The rule say you can apply 28 days before the ILR, then also remaining 29 days gap
I need advice on this situation if I apply the extension on 30th September 2025 I pay fee and then after 29 day I pay again fee for ILR.
If we write cover letter to secretary of state and provide all evidence and reason why she stay long time back home. So home many chances they accept our application.
Please advise me thanks