Hello. Thank you for contacting the Toolset support.
It seems we can filter the result of parent dropdown selector in one-to-many relationship by adding hook/filters but as you are using teh checkboxes field let me check your current settings and get back to you with possible solution.
Can you please share problem URL where you added the form as well as admin access details.
*** Please make a FULL BACKUP of your database and website.***
I would also eventually need to request temporary access (WP-Admin) to your site. Preferably to a test site where the problem has been replicated if possible in order to be of better help and check if some configurations might need to be changed.
I have set the next reply to private which means only you and I have access to it.