You're pretty much stuck with only having one active voicemail flow at a time, but you can always import a previous copy to restore functionality if you break it on accident. This is a scenario where having a developer org is handy, so you can test away without worrying about breaking something company wide. We've made a few tweaks to our VM flow and have not had any issues - the real trick is to be extra careful, test heavily, and when possible start in a dev org.
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Brad Murlin
Zillow, Inc.
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