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We are experiencing the same thing both on Alteryx Designer and Alteryx Server.
We have email event "After Run" set up for all our flows. Most of the flows have no problem except this particular flow runs more than 1 hour is experiencing this "Weird Server Reply" error. If I put some of tools in a container and disable the container to cause the flow finish, say 20 minutes, then the problem goes away. It seems to relate to how long the flow runs.
Also, if I add an email tool at the end of the flow, then the email tool experience the "Weird Server Reply" error but the "After Run" email event gets executed without error. So, it seems the first email action takes the hit, then, subsequent email action gets run ok. I can do this as a workaround, at least I will get the "After Run" email.