Sync deletes tracks from manually managed iPod touch
The iTunes sync function is deleting tracks from a manually managed iPod touch. This is occurring on iTunes 12.2 with a latest generation iOS 8.4 iPod touch.
I would rather not ever use sync, but it seems I must use it to update playback metadata on tracks. After using sync, I am seeing the dreaded issue where a significant number of tracks have a cannot find exclamation point icon next to them. The tracks are effectively deleted.
How can I stop this from ever occurring again? I have the following disabled in iTunes Preferences: Show Apple Music; Sync playback information across devices; Sync podcast subscriptions and settings; Automatically download album artwork; Keep iTunes Media folder organized; Copy files to iTunes Media folder when adding to Library. I have the following enabled: Disable: Apple Music Connect.
iPod touch, iOS 8.4