I've had a couple of problems deleting from handheld while syncing with iRiver H340 using v11.1.113
1.
Using Options > Handhelds > "Sync Mode -- Playlists", I synchronise to a smartlist which filters out files I don't want on the handheld based on a tag.
Under Advanced Options, "Delete from handheld any files that are not in sync list" is checked.
The problem is that a number of files appeared in the sync list twice: both in the queue and as marked for deletion. The reason seemed to be differences in the tags between versions on the PC and handheld. The files were not being deleted and therefore appeared in the list before each sync. Physically deleting them from the handheld solved it but I think this should be automatic.
Maybe it's copying the file first and then deleting the very same one afterwards?
2.
The other problem is that other non-MediaCenter files were deleted during the sync. For example, the handheld has a folder for its own voice recorder and this was deleted. It would be preferable for the deletion to occur only below the folders specified in the Advance Options Files & Paths.
3.
Small issue.
I created a visualisation which uses the variables PN_POSITION and TOTAL_TIME. These both change to the next song's values about six seconds before the current song has stopped. This was fixed some time ago for the text in the player but seems to persist in visualisations.