Internal links changed after fresh OS install

I reinstalled MacOS.
Copied my Obsidian vaults.
All of the internal link formats have changed.
All my internal links went from [[]]
to

For example
Links which were:

[[Effect of Cocoa and Its Flavonoids on Biomarkers of Inflammation Studies of Cell Culture, Animals and Humans - PubMed]]

Are now changed to:

[Effect of Cocoa and Its Flavonoids on Biomarkers of Inflammation Studies of Cell Culture, Animals and Humans - PubMed] (app://obsidian.md/Effect%20of%20Cocoa%20and%20Its%20Flavonoids%20on%20Biomarkers%20of%20Inflammation%20Studies%20of%20Cell%20Culture,%20Animals%20and%20Humans%20-%20PubMed)

How do I revert the links to the internal link format [[]] without having to do them manually?

How exactly did you proceed? Did you (after reinstalling MacOS) copy your obsidian vault backup including the hidden .obsidian folder? Did you install any community plugins before opening your vault for the first time?

I copied the obsidian vault but I was not aware of a hidden .obsidian folder.
I remember updating community plugins when opening the vault for the first time on the new install.

Please reply to that question first - it would help giving some advice without writing a complete help document…

Just in short: The above-mentioned hidden obsidian folder contains not only your themes, css snippets and plugins, but also all of your custom settings. It is a subfolder of your vault. If you include it in your backup, obsidian - after reinstalling - will open your vault with exactly the same settings (including link formats) as before.

“How exactly did you proceed?”
I copied the vault folder to a flash drive be fore reinstalling MacOS. Then I copied that folder to the new install and opened it.
On first opening I was asked about safe mode and updated plugins.
I was not aware of any hidden files but there is a .obsidian hidden file in the vault now.

Are you using any community plugin that converts the format of your internal links? Which link format is set under settings → files and links?

I hope the backup of your vault still exists - if so, all you have to do is to delete the local copy (!) of your vault, then adjust your settings as desired, re-copy your vault’s backup to your local file system and open it again as a vault.

(Files and links)
New link format - Shortest path when possible
Use Wikilinks (ON)

(Community plugins)
Admonition
Better Word Count
Mind Map
Sliding Panes
Tag Wrangler

I do not have the backup.

Going through some other older notes here and their link type has not changed. This might not be a universal issue that occurred with the reinstall. It seems to be just a few files, which is not such a big issue to fix manually.

Thanks for your help alltagverstand

You should always, really always have a backup of your files!

In this case, all you can try is using a plugin like for example this one (have never used it myself) and try to reformat all your links.

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Thank you