I am currently working on a project and using the default WordPress Editor I could see the custom fields I was defining. I later decided to enable Gutenberg Editor as this is needed, however the custom fields I defined are no longer showing. I also went to Gutenberg Editor > Preferences > Panels > Toggled Custom Fields, however after saving and opening these preferences again, it seems that the option was not saved.
If it helps, I have the following supports when defining the CPT:
'supports' => array('title', 'editor', 'author', 'thumbnail', 'excerpt', 'revisions'),