Setup:
PC Running Flash FXP
360 Running XeX Menu 1.1 FTP
I'm Running it from a Disc Cause I'm trying to FTP the Content Folder from my XBL Drive, so i can patch my content to my modded system, but allot of folders are failing to transfer, from in XeX Menu i don't see anything in these Folders(havn't checked them all), they seem empty, but some empty folders do transfer. This Drive has come off a 9199 XBL system, and the modded system is running freeBOOT 0.32 9199, so that the XBL drive wouldn't try to update the modded system.

Just wondering if theres new content protection from MS on the drive from the new update, or just software issues on my end

Error says Path Not Found in Flash FXP

Are you trying to ftp your profile?
If yes, you need to disconnect from it before any file operation otherwise it will fail.
You can't copy a file while it's beeing used (file privilege errors).

XBox Guide -> Profile -> Disconnect and then go ahead it should work.