Please check that the account's Deleted folder is properly mapped to a server folder.
- Long press on the account on the app's main screen
- Options and folders -> Folders
- Wait 10-30 seconds for the app to refresh the folder list
- Find "the" Deleted folder ("Deleted Messages", just "Deleted", "Trash", "Bin"... can vary.. for Gmail it would be under "[Gmail]" or "[GoogleMail]")
- Tap its name, choose "Sync as Deleted".
You may want to check Drafts and Sent as well while you're on that screen.
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What probably happened is - the app's database got corrupted and the app restored basic account settings (but server folder mappings are not part of that... maybe it should be).