A problem that I believe happens (at least with gmail accounts) when you undo a delete is caused by how gmail handles the inbox. “Inbox” is a label for gmail. When you delete the email, it gets moved to the trash, and the label “Inbox” is deleted. When you undo the deletion, the email goes out of the trash, to “All mail”, but doesn’t recover the corresponding “Inbox” label. Then, the email would appear in “All mail” (maybe called “Archive” inside mailspring) but not in the inbox.
See "Undo Trash" does not return mail to Inbox
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