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With the new teams, links in email are trying to open the classic teams. Also, when chatting, i get emails telling me i missed chats, but i only missed in "classic" not new teams
Odd about the e-mails. That sounds like a bug.
As for opening the links in old Teams. You can go to your Default Apps in Windows and modify what opens the ms-teams links etc. there to the preview client if you prefer that and remove from the classic client.