Maybe I wasn't clear enough.
All the sections and the TOC are the same in the copied campaign. When using a custom anchor I only put in #anchorname without anything related to an absolute path.
The exact same thing happens when using autogenerated TOC. No absolute paths when editing.
Example: If I copy a simple html page with relative anchors the copied version will never link to the original but stays on the page. That is expected.
Except when campaing is copied my simple relative anchors are rendered with the previous campaign ID, which I couldn't have possibly include when creating an anchor.(no option for this in editor) Hence one is expecting ID-s to be generated respectively...like in the autogenerated TOC.