So I finished syncing my large collection. It failed several times, mostly for the unknown reason I posted before. Once because my computer went to sleep.
Performing the sync several times seems to have gotten it to work correctly. The only error is one song that keeps trying to copy everytime but won't for some reason. The log shows it copying, but it never makes it to the sdcard and both say the sync was complete.
Copying it over manually and then resyncing it again matched the expected results.