Removing some of the checkbox values will not alter posts that are already saved, but it will alter them if these posts are edited and updated.
You might want to look at using an acf/load_field filter https://www.advancedcustomfields.com/resources/acf-load_field/
In this filter you could alter the choices dynamically, only removing the ones you want to hide if they are not already selected for the post. The choices for a checkbox field work the same as the choices for a select field https://www.advancedcustomfields.com/resources/dynamically-populate-a-select-fields-choices/
