Deleting all items from nav tree leads to NPE

When you remove all items that can be removed from workbench navigation tree (Go to Dashboards > Navigation and click "trash" icon for the for groups under "Workbench" group) and you save the tree there's "Cannot read property ‘c’ of null" shown.

Trying this with workbench with unobfuscated stacktraces shows that the issue is coming from this method

I'm attaching video showing steps to reproduce as well as screenshot of chrome dev-tools javascript console (unobfuscated stacktraces).