Try naming your "new" files with the same name as the "original" ones. I'm not sure how the carrier customization handles these files. But I'm just guessing it might still be looking for the specific file names.
I do know this for fact (as it worked for me): You don't need to put a blank MP3 there to remove the boot/shutdown sounds. Simply removing the original files (I put ".bak" at the end of the file name) will kill the sounds.
Also, for whatever root explorer you are using, be sure you mount the directory as R/W when writing or changing files.
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Phone: HTC One X (AT&T version) Rooted, Bootloader Unlocked, S-Off
Tablet: Samsung Galaxy Note 8 (WiFi only) Rooted