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Try clearing the immutable bit with chattr -i badscript.
Oh, and if someone can write files to the /root directory of your server, you have bigger problems than a stubborn script file. Someone has managed to get root access to this server.
First thing to do is remove the computer from the network. Then there are plenty of guides to get you through the cleanup if you DO NOT have a good backup.
also remember that stat/lsattr/getfacl are your friends for permissions issues.
Changing the root password isn't going to change the fact this was a root compromise. If this was a production machine then alert any users (have them check their machines as well), mark backups "tainted" and not to be used, isolate all network access to your management IP (range) and investigate with the intent to learn from it, set up a new machine and follow proper procedure (that is, not with the intent to try and "fix" this "victim" machine).
*As an aside I always though you asked too much questions in too little time and without properly discussing replies and options, but maybe that's just me.
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