DNS problems with public navigation settings

I hope I can describe this well:
We have officially connected the DNS of our server to www.verhalenbank.nl. The only problem now is that when Omeka detects that there is no longer a /vb/ (subdirectory in which the omeka instance is located) in the links of the navigation settings, the default settings are used. This scrambles up the public navigation. Also, a manually added site will not be found through the new URL.
I think this is due to the static nature of the links once they are saved in the settings. This makes it impossible for modified Omeka instances to be accessed from multiple domains.

I get the situation you're describing, but I'm not sure of the consequences you're seeing.

Is there an error, do the pages lose their ordering, or does something else happen?

I don't see an error anywhere. JWhen I access our website from another domain, the navigation refers back to the default settings. It does show the manually added sites, but the link is broken. It also shows the default links that I deselected to be shown.

When I set the menu values In the admin site of our server (x.x.x.x/vb/admin), the navigation is scrambled on www.verhalenbank.nl. When I set them on the admin when accessed through www.verhalenbank.nl/admin, the navigation is scrambled on x.x.x.x/vb/.
This is because /vb/ is added to the links on one domain, while this is not the case on the other. I'm not sure if there is anything to be done though. For now we only access it through verhalenbank.nl.

Yeah, unfortunately I think this is just a restriction built into the way the Navigation component works, since it saves root-relative URLs, not Omeka-relative ones.