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As of FreePBX 2.10, Music on Hold files can be managed entirely from the command line with no adverse effects.  You may find it easier to upload and move files from one category to another by using SSH to access your machine and then using scp to upload files, and cp or mv to copy or move files into categories.  When you're done, issue amportal restart from the command line to restart Asterisk and FreePBX and have them rescan the Music on Hold Files.

User Guide