Reference style links are not supported, and lead to odd behaviors. There is a bug report in the forum, so it is at least known. (It's non-trivial to support for a variety of reasons.)
My current solution is to copy and paste the link every time I reuse it. It has already led to mistaken links I don't catch, etc., so hopefully I can find a better solution soon.
If you edit a header manually, it will not update anywhere you have referenced that header. This results in dead links.
The solution is to right click the header when you want to edit it. In the dropdown, choose "Rename". Doing it that way will update it everywhere it is referenced.
That same dropdown will allow you to do other powerful things, like extract headers in to new notes, or extract selected text in to new notes.