To recreate, go to a site with Gutenberg installed and activated, as well as Toolset with a CPT. Create a new post and add the Custom HTML block. Type some text and then click the button above the Fields and Views button above the block. Insert a shortcode (post title, author, or a field from your CPT). The text that was already in the block is deleted and the block remains empty. It does work if you insert the shortcode using the steps above into a block with no content.
I have tried it on a couple of sites. I don't think you need site access to recreate, but if you do I can add that.