How to save entity from a ajax form
Drupal 8 doesn't cache Ajax forms anymore, so you can't get properties of the form object set in the initial form build. see Bypass form caching by default for forms using #ajax.

Forms are only cached as rendered form. Put the entity id in a hidden form element to load the entity before saving. Add the entity cache tag to the form if you use default values from the entity.

Or consider to switch from a general Form API form to an entity form.