Here’s an interesting wrinkle. It’s not bad and it’s a bit of a specific slog to get this to show up
Create a new database. Add a markdown document named “doc 1”.
Add a second markdown document called “doc 2”. Add an annotation containing "related to " followed by doc 1’s pasted item link.
Click on doc 1 and activate the see also inspector.
Doc 2 will appear in the see also list. Click on it. Doc 2 is now displayed in the main edit window.
Now switch to the annotations inspector. The annotation will be gone.
Hit command-r. The highlighted entry in the nav panel will switch to doc 2. The annotation will still be blank.
Click away from doc 2, perhaps by clicking doc 1 in the navigation list. Now switch back to doc 2.
The annotation is safely back.
The annotation also reappears if you switch the markdown view from preview to source.
On a side note, annotations have become very handy lately. I use them to chain notes on one phone call back to the phone call that preceded it, and I also sometimes make a little map of contents for a document in its annotation.
I’m running Devonthink 3.9.2 server edition on MacOS 12.6.8 on an aging but faithful late 2015 iMac.