Migration cycle fails with externally modified exception

While trying to upgrade my content with a new version of my cnd. I run an upgrade module, which terminates my upgrade cycle with the attached stacktrace and leaves my repository in a useless state.

As a side note: The update went fine 2 out of 4 times.
Side note 2: We had the CMS console open with /hippo:configuration/hippo:initialize/hippo:version open.