I use an extra dnsmasq config file to redirect local lookups to a local authoritative resolver (bind9 running on another box). Will switching to FTLDNS break this, and if so, how would similar functionality be configured with FTLDNS?
No, FTLDNS is designed to be completely transparent and allows all customizations users might have set up with dnsmasq. It will read all config files and act accordingly. However, if you want to be 100% sure, you can join our beta testing. It has the enormous advantage of us being able to push out small changes (typically bugfixes) without having to wait a long time for them to come with the next release.
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Thank you—I believe I shall! 
edit - And now that I'm actually reading the blog post I see that you guys answered my question in the post. D'oh! Apologies for that.
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