I highly doubt Charles Proxy is a problem. It's exactly what its name implies: a proxy. Without some advanced wizardry, you won't be sending any data from the EQ client through the local proxy app and then onward to the EQEmu servers.
It's no different than running Wireshark at the same time. And if running Wireshark at the same time as EQ gets you flagged/banned, then I'm hosed. I use it on a daily basis for my job, for debugging personal apps, etc. I've not ever had any trouble.
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