I encountered this issue while making a copy of a Site Collection in the same farm for testing purposes. The Site Collection in question was using Managed Navigation.
The fix is, luckily, quite straightforward. Go to Site Settings > Navigation and change Global Navigation and Current Navigation to “Structural Navigation” and click on OK.
Now go back and change Global and Current Navigation back to Managed Navigation and click on OK.
It may not appear to be resolved immediately, but refresh the page and you will see that the Managed Navigation is back up and running.
While this will work when migrating a Site Collection to another Web Application, be warned that the original site collection’s navigation, if left as Managed Navigation, will now be broken instead.