This was fixed in the upload of update-manager 1:0.156.12:
update-manager (1:0.156.12) precise; urgency=low
[...]
[ Michael Vogt ]
[...]
* remove skype from the removal blacklist
update-manager will now be able to complete the upgrade, even if skype
must be removed in the process. The skype package can be reinstalled
immediately after upgrade.
** Changed in: update-manager (Ubuntu)
Status: Triaged => Fix Released
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https://bugs.launchpad.net/bugs/982859
Title:
Upgrade from 10.04 to 12.04 breaks if skype is installed
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