Update to post-- I'm using the Runtime SDK for Mobile v3.1, not v10.1.
The FeatureLayerSyncAgent doesn't seem to have the features ordered in the same way as the mobile cache. I tried to get the index based on the mobile cache:
mobileCache.FeatureSources.IndexOf(_mobileCache.FeatureSources[layerName])]
But the index order appears to be reversed--the last item in the MobileCache matches the first item in the featureSyncAgent. In the code, we've customized sync to download only certain features, but we accessed those by name in Mobile 10.
Has anyone else run into this issue?