It seems that after a lookup that is in DropDownMode is initialized changes to the LookupPrefilters have no effect. The items are cached and a check is done to not reload the list if any items exist in the list. Since the list is cached a new call to LoadItems will not be made.
Luckily with a little reflection magic this can be resolved. The following code is a method that can be called that will clear the items and allow it to be correctly refreshed in case of a change to the LookupPreFilters
Have an excellent day