The Airbus A330 plane was carrying 194 people at the time of the incident.
Entire workforce could have contracts terminated on June 1, with just two-thirds to be re-hired under new conditions.
Meanwhile, Emirates Airline posts $1.25 billion profit for the financial year to March 31, up 40 percent from last year.
The British-born Flanagan, who launched the airline with $10 million in 1985, had retired two years ago.
A breakdown of Emirates Group's $26.3bn revenues for the 2014/2015 financial year.
Doha carrier says lower growth was due to "complications" with the A380 and 787 Dreamliner deliveries.
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