I have a content type with an entity reference field referencing to a custom entity. I need to use a select box because an autocomplete widget is not suitable in my case. However, I cannot load all the entities at once as selectable values because they are too many (72000+ the form won't even load). So I default the entity reference select box to a limited number of values using a views filter and then hide it by default. Then I use an ajax dependent dropdown to show and populate the entity reference select box with filtered down values (I'm using a module that implements hook_form_alter).
My problem is that the form won't validate because now I can select entity reference values which are not the default ones in the select box. So I guess I should control in some way the validation rules of the entity reference field. Is there an easy way to do this? Which hook should I use?