♪
No, will not overwrite your music files.
Update just overwrites the rockbox.ipod file, and .rockbox folder and subfolders, but keeping your "extra" personal files as eqs presets, cfgs, wps themes, databases (tagcaches), etc...
When updating, you can extract the zip file on the player's root folder, and when asking to substitutes same existing files, click on Yes To All.
The job will be done automatically.
♪