The AutoComplete control takes control of its source collectionView filtering in order to show only items that match what the user typed.
If you want to keep control of the filter, set the itemsSource property to your CollectionView's items property. The AutoComplete will create a new CollectionView for its internal use, and the original filtering will be preserved.
For example, the AutoComplete below uses a filtered CollectionView as its itemsSource. The filter remains active while searching for items as the user types: