This is a reply someone on the SYNC forum got from Ford regarding the indexing limit:
"While there isn't an exact number for the maximum amount of songs that SYNC can handle, the capacity for SYNC is about 20,000 songs. This is assuming that the compression rate for these tracks would be at 128-Kbps. The higher the compression rate (192-Kbps, 320 Kbps) the smaller the number of tracks Sync can handle.
Just as with any other device, we cannot guarantee compatibility (because it is not on our device list). But as long as the device is formatted FAT32 and can be powered through USB (or you have some other way of powering up the device) it should work like any other mass storage device. NTFS does NOT work as a partition, it was thought to have, but was discovered not to work. Note the recommended maximum capacity for any media device is 100GB (again, not saying anything more will not work but that is the recommended maximum for reasonable SYNC performance).
SYNC has a limit of 15,000 grammar objects. After SYNC completes the indexing of songs, it begins creating the set of grammar objects or voice commands. Each song can have up to 4 commands associated with it, one each for: Genre, Artist, Album, and Track. Repeats are not counted, so if you have 100 songs by the Beatles, the Artist name "the Beatles" only counts as 1 toward that 15,000 total.
If the total number of voice commands would be over 15,000 at any time, the least specific group gets removed first. This is why your Track commands were disabled. Having 17,000 tracks would instantly put you over that limit, but grouping things by Genre, Artist, and Album gives less than 15,000 total. Depending on the diversity of your collection, reducing the track count to somewhere between 10,000 and 13,000 should restore the ability to use track commands."