I notice that a few of my internal links are of the format [Mynote](app://obsidian.md/mynote). In this example I cannot open the “note name” link directly by clicking on it. However, if I go to File Browser I can open “mynote” by clicking on it. I certainly don’t recall deliberately using the above format when I created the problematic links.
Added backticks ` around your link so it displays properly in the forum.
For internal linking,
Obsidian supports the following link formats:
- Wikilink:
[[Three laws of motion]]- Markdown:
[Three laws of motion](Three%20laws%20of%20motion.md)
The (app://... looks similar (but not the same) to an Obsidian URI or a mac shortcut. Maybe a plugin created it? 
Thank you for the information. Out of all my internal links (I didn’t count them) I found 16 instances where there was this unusual type of link. I went through each one of them and changed them accordingly.
I see no pattern in what or why these changes took place if it was a plugin that created them. What worries me is a possible recurrence of the problem as I do not know the cause of it.
Yes, that is worrying.
Have a look through your plugins and see if there might be anything about app linking, URL schemes, links, etc.
Also, I know you already changed them (ha!), but try to think again: were they created around the same time? Was there anything creating them for you?
I may try to investigate using an older backup, but I’m not too optimistic about it.
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