This happened in 2 different projects:
4.4.6 with the update training modules
4.4.9 plain ee bundle

The branding area in the default template prototype is in fact missing 2 subareas: logo and search
This results in a broken layout with some white space on top, will attach a screenshot in the case of demo-project.

The report doesn't show any error regarding problems with moving/merging the branding area.
From ETK:
[ok] Migration task: Migrate ETK configuration repository
[SYSTEM] Move and merge node from '/modules/extended-templating-kit/config/sites/default/templates/prototype/branding' to '/modules/extended-templating-kit/config/sites/default/templates/prototype'