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Apple Mail does have its share of bugs particularly on iOS 13. Personally, it was working OK for me on iOS 10 but became problematic starting with iOS 11 or 12, iirc.
That said, depending on the setup, some email may not actually be backed up to iCloud/iTunes. Gmail for example just re-downloads directly from Google's servers.
I use Gmail and I've noticed Apple's Mail app doesn't always sync changes to Gmail's IMAP servers (or at least it doesn't do so in real time) so I only use it for reading email and not organizing.
Thankfully, Gmail on iPadOS Safari gets the Gmail desktop website version now and is more or less functionaly. That's what I use when I need to clean up my email.
Mind, it's really more of a restore than a straight up clone. For example, Dropbox free version now limits you to three devices. If you clone a PC HDD, the clone still counts as one device. If you restore from iCloud backup, Dropbox counts it as a different device.
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