There are loads of fixes being done in the latest betas of both MMW and MMA. So this may have been addressed already and I'd recommend trying it from the Beta forum. You don't need MMA for Android sync.

Should I have used the Sync option in MMA, or had it open while using MMW?

MMW 4.1.17.1840 and presumably the latest version of MMA (Marshmallow with automatic updates). The playlists were synced to the SD card (via the phone, not directly) over USB using the WMDM plugin. I have uninstalled MMA as it was emptying MMW-created playlists somehow, and I don't need it.

Which version of MMA and MMW?

I'm having the same problem (on a Huawei P9 Lite). The playlists from MMW show up correctly in a third party Android app, Cross DJ, but once I open a playlist in MMA, it'll only show 5-7 songs. Cross DJ reflects this as well, and the only way to get MMW to auto-sync the playlists again is to modify them on my computer. I've uninstalled MMA for the time being.