Hmm. If it isn’t there, you shouldn’t be getting it.
Starting with the obvious - you’ve verified the templates are found for the export? By that I mean, did the output change to match your changed template (at least the top portion of it)?
Did you set up a template for Zotero Note Template.md? The default there has this link, since the idea is (if you export multiple pages) it will link back to the main ‘metadata’ document.
If not, add it. You’ll want to make it simple, since you’re just essentially adding it to the bottom of the ‘Mdnotes Default Template’
In the Docs regarding single files, it suggests this as a note template:
{{tags}}
{{related}}
{{noteTitle}}
{{noteContent}}
no other headers or styling, since again, this is just added to the other file
Mine is a little different. I like having an hr line to separate the notes (I have ‘related’ on the default note, no reason to double up):
---
## {{title}}
{{noteContent}}
tags: {{tags}}
If you still have issues, please share the contents of your templates Mdnotes Default Template.md and Zotero Note Template.md and I’ll have a go at them.
Good luck!