When using an end gateway in the End dimension that teleports you very far away (probably any unloaded chunk), the server no longer recognises you as an entity (selector @e[name=<player name> found nothing) and you cannot use elytra until you reconnect to the server. Tested in overworld air superflat and this did not happen (so possibly this could happen in the Nether or the Overworld as well if the server has to work harder to load the chunk, I haven't tested this).
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Yes I have tested just using /tp, and it worked fine, only happens when walking into end gateways. I'm thinking of making my end gateways useless and then putting a repeating tp command in that teleports you when you step into the gateway to get around this.
Have you tested this with simply /tp-ing? this might just be a bug regarding unloaded chunks.