How do I edit Managed Client preferences without them getting replaced? Specifically I would like to edit com.apple.applicationaccess.new.plist. (Which is in /Library/Managed Preferences/[username]/), but when I restart the computer my edited preferences are replaced with the old version.

How do I go about editing them for good? I only have command line access via SSH.
Turns out that the master copy of com.apple.applicationaccess is kept in /private/var/db/dslocal/nodes/Default/[user].plist. Editing that solved the problem for me. Thanks to Lyken for helping me find this on this question.