This is fixed in 0.4.2 synced into Ubuntu by MVO (thanks!).
It needs a follow on 0.4.3 which already is on the way.
** Changed in: apt-clone (Ubuntu)
Status: Triaged => In Progress
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https://bugs.launchpad.net/bugs/1902830
Title:
autopkgtest fails in hirsute - test_clone_upgrade.py
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