Keen had been due to compete in the championship decider alongside Cottingham in 2 Seas's #4 Mercedes-AMG GT3, replacing regular driver Jonny Adam who is unable to race at Donington due to a European Le Mans Series commitment.
Together, Adam and Cottingham lead the British GT3 standings by 13 points having taken three wins and a further two podiums this season.
But Aston Martin factory driver Adam, who already has four British GT titles to his name, will be absent despite attempts being made for him to race at the season finale.
Keen, who currently shares the British GT wins record with Adam, had previously been announced as racing in the Scot's place earlier this season.
He has already competed in the sister 2 Seas machine in Portimao alongside reigning champion Ian Loggie, filling in for Mercedes factory driver Jules Gounon, and had tested with the team and Cottingham at Donington earlier this month.
But the Anglo-Bahraini squad announced on Wednesday that Ellis, a Mercedes factory driver since 2021, would instead fill the role alongside Cottingham.
Source: Autosport