Backup & recovery of e-mails including folder structure and labels
The export tool and the import-export app need the ability to keep the folder structure and labels.
After having to restore hundreds of lost e-mails during an account migration I just discovered that the export tool appears to export all emails but not their location (i.e. sent and received e-mails all appear in one folder, and no folder structure whatsoever is exported). Furthermore, the import-export app only allows to restrict an import to a specific time period, but it does not allow to import certain folders from a backup back into the correct destination folders and using the correct source labels.

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J. C. commented
The new CLI export tool does export all e-mails to one folder as EML files. However, it also saves a JSON file of metadata for each message, which includes its folders and labels.
I have not yet had to recover a Proton account from its backup, but I would certainly hope that the CLI tool correctly reads and applies all of that metadata when importing.