I may not fully understand the linking options, but when the last item in a list is a yes/no question (or probably anything with a link in it), when the link is executed any unchecked items in the current list are ignored.
For example, in a pre-takeoff list there may be a question at the end: Skip de-icing configuration? If Yes is selected the intent is to jump to the final takeoff list; if No is selected the intent is to proceed with the next list, which is the de-icing configuration list.
However, when either Yes or No is selected, any unchecked items in the pre-takeoff checklist are ignored, and the user is taken directly to the linked list. The result is that linking seems to defeat the functionality which reminds you to attend to any skipped items in the current list.
I think a work-around for this example might be to put the Yes/No question at the beginning of the de-icing configuration checklist, rather than at the end of the preceding pre-takeoff checklist. But is there a setting which would invoke checking for incomplete items before executing a link?