"KillMutex" is a keyword in HotkeyNet's script language, so apparently you're asking a question about the use of HotkeyNet without naming the program.
You're also asking a general question about deleting DAOC's mutexes or running more than two DAOCs on a single PC.
So far as I know, Mythic has never said anything about either of these questions.
With regard to the use of HotkeyNet for this purpose, I don't think it's safe to run HotkeyNet and DAOC at the same time because there is reason to believe, based on player reports that have been posted on HotkeyNet's forum, that Mythic is using the presence of HotkeyNet to identify violations of the rule against multiboxing. I understand that you are not using HotkeyNet to multibox but if Mythic is simply looking to see whether HotkeyNet is running, then it doesn't matter what you are using it for.
I suppose you could reduce that risk by running HotkeyNet for just a few seconds each time you launch DAOC, just long enough to execute KillMutex, but that's inconvenient.
Since you are using HotkeyNet only for KillMutex, I would suggest that you use LottaCam instead. LottaCam does the same thing as HotkeyNet's KillMutex command, but that is the only thing it does. So far as I know, nobody has ever been punished for using LottaCam. LottaCam is more convenient than HotkeyNet because you simply launch it and forget about it until next time you reboot.
I wrote both of these programs so I have no axe to grind here. I'm just recommending the safer and more convenient of the two.
http://www.daoc-trophy-mobs.com/lottacam/lottacam.html
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Author of Mojo
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www.gaheris.net
www.daoc-trophy-mobs.com
Former PvE server team lead (2005)