Some issues in chechbox functioning

I have developed code for my structure using Luca's answer logic for my question asked here: For selected items from popup toggle div code . But I am getting some issues which I am unable to solve.

I have used 'Update' and 'Cancel' buttons on my popup instead of 'Done' as shown in images. 'Update' button is functioning same as 'Done'. 'Cancel' is used for just closing the popup.

My updated HTML and script code is here(please ignore the result of fiddle, used for just code): http://ift.tt/2ab8Mrx

I am getting issues with family member pop-up which is shown in Image5 in my previous question. 'update5' is id used for 'Update' button this family member pop-up.

Issue 1: When I add family members for the first disease(selected from Image2 in my previous question), they also show up for the second disease. e.g. In Image6 in my previous question, 'Grandfather (maternal) and Grandfather (paternal)' family members are selected for disease 'Asthma'. When I want to add family menbers of 'Alzheimer Disease' then 'Grandfather (maternal) and Grandfather (paternal)' these options are already remain selected. That shouldn't happen.

Issue 2: Suppose 'Grandfather (maternal) and Grandfather (paternal)' family members are selected for disease 'Asthma'. Now I want to 'Edit' family members option like if I deselect 'Grandfather (maternal)' and click 'Update' then its updated. If again I want 'Grandfather (maternal)' option for 'Asthma' and select that option then it doesn't come on page for second time after deselection. That shouldn't happen.

I tried to solve issues by clearing all checkboxes of family member popup before closing this popup but its not working.

Can anyone please help me to solve these issues?