It didn't exactly blow up, but it's still not right. The one issue I have left to resolve is scripts in menu folders (like the the Clippings Folder and Scripts Folder in SD). The file names use numbers followed by a ) in order to sort the menu choices.
In this environment users are able to sort these menus to their liking, based on their most common tasks and preferences or whatever.
In its current format the syncing system doesn't see a file with the same name and copies it, but that means we end up with duplicates because the file was there but with a different number in its name.
Now I have to write a routine that will ignore the number part of the file names and just compare the root part of the file name, and if a file needs to be synched it would replace the file using the full name on the user's machine instead of the name of the file's source.