Read these Wiki articles. Again. Thoroughly.
https://wiki.jriver.com/index.php/Sync_Handheld https://wiki.jriver.com/index.php/Handheld_Sync_OptionsFirst, when you sync using the two different methods you mention, MC thinks you are syncing to two different devices. Hence, it can't manage the files the way it is supposed to and will see files synced using one method as not required with the other method.
Maybe you could work around the issue, but the easiest thing to do is select one method and always use that. Always syncing to the microSD card would make sense.
However, for small uploads, I plug my V40 plugged in via USB but then all of the m4a files are flagged with File Not Supported. (see pic).
Then you probably don't have m4a files included in the "Files, Paths & More > Supported Types" Handheld Sync setting, for the sync to phone method.
MC won't move forward without removing those files from the sync.
Because they are part of a Sync to a separate device, your microSD card. See above.
Note: You get different options for different device types. i.e. A microSD card inside a phone connected via USB will show an option "Delete from handheld any files not in sync file list".
Also, I'm finding that if I change some properties, such as Genre, it's not updating those existing files with the new properties on my phone after the sync. Should that be happening?
Options > Handheld > Resync if date modified has changed.
Make sure you are writing those tags you want to see updated on the phone to the audio files. Genre, as an example, is written to audio files.
"Options > Library & Folders > Manage Library Fields > {select a field} > Save in file tags (when possible)".
"Options > General > Importing & Tagging > Update tags when file info changes".
