I have the same issue as #3355 has.
Marking an email read... few seconds after a click

Email marked back to unread... after I clicked 'okay' on the error message

What operating system are you using?
macOS Sierra 10.12.6 (16G1114)
What version of Nylas Mail are you using?
2.0.32
Do you have any third-party plugins installed? If so, which ones?
No.
Is the issue related to a specific email provider (Gmail, Exchange, etc.)?
I guess, Gmail. I have 5 accounts (4 of them gmail) connected but the anomalia is only with one email. If I remember correctly then the issue began when internet was unstable but I can't say anything for sure.
Does this feature exist in another mail client or tool you use?
No.
Any ideas what now? It's quite annoying as you can imagine 😄