Hi,
could you add to the apparmor profile of charon this line
   @{PROC}/@{pid}/fd/ r,
Then reload it via:
   sudo apparmor_parser -r /etc/apparmor.d/usr.lib.ipsec.charon

While I never have heard of charon needing this, if the above works you
could add it for youself as a config and I could make it part of future
packages.

If the above makes those messages disappear but shows new apparmor
denies afterwards let me know.

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https://bugs.launchpad.net/bugs/1786250

Title:
  strongswan (charon) is rejected by apparmor to read /proc/<PID>/fd

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