Uplink,
90 days do include Visa Cancellation. On your very last day you get your passport back, hand in your ID & Medical cards, and get your final settlement.
Friends have left the following day, but did find it very stressful. I left 2 days later instead, which I meant I didn't have to run around like a headless chicken.
All in all the EK side of leaving and repatriation was handled very well for me. I do suggest booking a meeting with your leaving coordinator early on. That helped me clarify a lot of questions. The same team were also readily available on phone and email.