Odd, after I posted that I was searching and then found this.
http://www.fordservicecontent.com/Ford_Content/Catalog/owner_information/Lincoln-SYNC-3-Supplement-version-2_sycsy_EN-US_02_2016.pdf
"Supported Media Players, Formats and Metadata Information The system is capable of hosting nearly any digital media player, including iPod, iPhone, and most USB drives. Supported audio formats include MP3, WMA, WAV, AAC, and FLAC. Supported audio file extensions include MP3, WMA, WAV, M4A, M4B, AAC, and FLAC. Supported USB file systems include: FAT, exFAT, and NTFS."