Custom Post Type, Saving Multiple Checkboxes

You will need to save them as an array and currently your HTML is not in the correct format to do this.

<label for="my-cpt-32">
    <input type="checkbox" name="cpt_ids[]" value="32" id="my-cpt-32" />
    My CPT #32
</label>
<label for="my-cpt-41">
    <input type="checkbox" name="cpt_ids[]" value="41" id="my-cpt-41" />
    My CPT #41
</label>
<label for="my-cpt-43">
    <input type="checkbox" name="cpt_ids[]" value="42" id="my-cpt-43" />
    My CPT #43
</label>

When this get’s $_POST’ed you will have an array of checked values, make sure to check it is ‘set’ e.g. isset( $_POST['cpt_ids'] ).

If you ticked 41 & 43 you would get array like this:

array(
    [0] => 41,
    [1] => 43
)

which you can use to save in your custom field, or a secondary table etc.

I hope this helps!