The software problem initially impacted 209 aircraft, with fewer than 150 still requiring updates as of Friday night, expected to be completed by Saturday.
The carrier emphasised that safety remains its top priority and thanked customers for their patience during this unexpected event.
Delta Air Lines also anticipates some operational impact from the same software issue, confirming its compliance with directives.
This issue coincides with a chaotic period for US air travel, with over 3,700 flights delayed and nearly 100 cancelled across the country on Friday, as 6 million Americans travel for Thanksgiving.