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I have in the past seen flavoured whole coffee beans on sale. Here is an example (though it was a roadside market stall where I saw them).
Do you need to brew the coffee at a lower temperature, or otherwise prepare it any differently than you would do with unflavoured beans?
Here comes an unintentionally snarky answer:
Flavored coffee and high quality coffee are rarely synonymous. Since flavored coffee masks the organic and natural flavors of the coffee itself, it's rare that a quality bean is used in the first place. Imagine ordering a Glenlivet 18 with Pepsi.
Ergo, I'd say that your brew temperature with a flavored coffee isn't extremely important. In the end, you're really just going to be tasting artificial (natural if you're lucky) flavors that cover up the taste of the bad coffee underneath.
What I would say, however, is before you start using quality coffee after using flavored coffee, be sure to clean your equipment thoroughly. The flavors used in those coffees have a tendency to stick around long after they're gone.
