Thanks for the update.
I'm closing this report because this is the intended behavior. The
workaround is either to removed the manually installed package or to set
overwrite-local=1 in /etc/python/debian_config before running the
upgrade.
** Changed in: python-pysqlite2 (Ubuntu)
Status: Incomplete => Invalid
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package python-pysqlite2 2.4.1-1 failed to install/upgrade: pycentral
pkgprepare: not overwriting local files
https://bugs.launchpad.net/bugs/292479
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