Entity:media doesn't exist error when searching for url in "add link" in wysiwyg
I had a similar problem, but not with entity:media, but with entity:shortcut

I ended up by deleting the matcher from the database.

It is in the datatable config under the name "linkit.linkit_profile.ckeditor"

SELECT * FROM config WHERE name= "linkit.linkit_profile.ckeditor";

The data is stored in a serialized string. To remove it, you must be confident in editing serialized strings, which is a bit dangerous.

I used (UN)Serialize.me to convert the unserialized string to a JSON string, then edited the JSON in JSON Editor Online and back again.

I first tried to use drush to export the config, editing the config YAML file and then importing, but it yielded the same error.