I've noticed that with Gmail. I'll send something to the Trash in EE only to find it sitting in my Inbox in the browser. I can also only see/sort to one of my labels in EE, so something isn't communicating right.
I don't have a solution for you though, sorry. I kept switching between EE and the default email app before settling on EE & just never deleting or sorting my emails through the app.
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