Hi Sarah,
ACF works mainly as a GUI (and API) for post meta (and other meta) and as such does not attempt to delete any information on it’s own.
There are situations where it would be quite aggravating to have your information being deleted with ACF fields and there are some posts here already discussing this issue.
You might find this post interesting as it suggests a solution: http://support.advancedcustomfields.com/forums/topic/database-cleanup-feedback-on-function/
