I flew to the US via JFK on the 12th of November and left back to the UK on the 13th, my arrival is shown on the I94 website, but my departure isn’t.
I flew BA, and I’m worried that I’ll be flagged as overstaying despite being back in the UK.
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Please wait for two or three more days and check again. It is very likely to show your departure "in due course" with no action required by you. Meanwhile be sure to retain your boarding card. If after a week there is still no record of your departure see U.S. Customs and Border Protection which includes:
If you departed by a commercial air or sea carrier (airlines or cruise ships), your departure from the U.S. can be independently verified, and it is not necessary to take any further action, although holding on to your outbound (from the U.S.) boarding pass - if you still have it - can help facilitate your reentry next time you come back to the United States.
If you are a VWP visitor and you left the U.S. by an air or sea carrier, you don't need to worry.
We strongly urge you to keep a copy of what you send to DHS-CBP and carry it with you the next time you come to the United States in case the CBP Officer has any questions about your eligibility to enter. Carrying those materials with you will also allow your record to be corrected at the time of entry if, for some reason, the London, Kentucky office has not yet done so.