this is tracked at https://www.ventismedia.com/mantis/view.php?id=16149
We need to improve it in the future to avoid resetting paths without informing a user why it is happening.
It happens because you have on MMW side set paths without subfolders.
Verify it, go to
1)MMW/Tools/Options/Portable Device Sync, find your device and click to "Configure"
OR connect your phone via USB and select device directly
2) go to the Options tab and select "File locations", the default setting should look like for music
\Music\<Album Artist>\<Album>\<Track#:2> $Left(<Artist>,20) - <Title>
and I think your setting look like
\<Album Artist>\<Album>\<Track#:2> $Left(<Artist>,20) - <Title>
so MMA know that you want to sync to the root folder and that's why
MMA local setting which is set to "SdCard/Music" is ignored, because it is a subfolder of Root, which is required for synchronization.