Mouseflow is able to include Flash elements in heatmaps and playback sessions as long as they're part of an HTML page. However, Mouseflow does not currently track user interaction with them.
If you have Flash elements that don't require user interaction, Mouseflow will track them without any issues. However, if you have Flash elements that rely heavily on user interaction, then this may not be the best tool for you. Services like Google Maps are also difficult to track and you can read more about that here.