Since MacOS 10.11 (El Capitan), Apple’s Operating System features System Integration Protection or short SIP, which protects certain directories from write-accesses. This protection gets more thorough by the versions. This led to a bunch of mishaps when upgrading my laptop.
One of them was, Apple Mail could not access my Mail-Directory under ~/Library/, however, the visible errors where of the likes that the mail retrieval from my servers did not work…
It took a while to figure out SIP was to blame. Just add Apple Mail.app to Settings->Security&Privacy->Full Disk Access. Hopefully there are no bugs in Apple Mail that would allow it to read & write to parts of the disk — which otherwise would be protected by SIP.
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