Hi Seany77,
I'm on the 5 year spouse journey FLR(M) with my ILR currently in the process of application. I also am a director of a limited company and was so at the time of my last 2.5 year FLR(M) application. When I applied I received a letter stating that they needed more financial evidence and I needed to submit my most current CT600 as the financial year I used fell prior to the date of application. My application was made in November 2016 with my year ended on 31st October 2016. So although I wasn't required by HMRC to file and pay any taxes owed for year end 2017 until July 2018, I had to file my CT600 immediately. I simply explained my reasoning and asked that they wait a week to receive the current CT600. My application was successful in the end.
So my answer to your situation would be if you make the application before the end of your financial year, then they should accept that as proof of income. In the meantime I would immediately consolidate your books and file the earliest you can for your next financial year. Just in case they ask for that. They will be more willing to be accepting of your circumstances if you are proactive. You mentioned;
The reason I have this concern is that I have a correspondence from the UK Home Office concerning our first application refusal and it states that my wife ‘Applied for Entry Clearance’ on Feb 5th 2019. This was the date of the appointment at the Visa Centre, not the date of online application which was Jan 04 2019.
If 4th Jan 2019 is the date of your re-application then your financial evidence should be accepted.
On the other hand, the case worker will not be forthcoming of anything you may miss so you have to do all the research.
Hope this helps,
Hof