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. It is important to note that Flash is in the process of being deprecated and will no longer be supported by Adobe after the end of 2020. You can read more here.