If you're running Mercurial you should only have a 'default' branch rather than a 'master' branch (the latter being a git convention). Both of the 'flows' have a concept of a 'production branch' which is the one that you deploy - it defaults to 'master' on git-flow and 'default' on hg-flow, so this should all work out correctly with AppHarbor. Are you saying you have a 'default' AND a 'master' branch? If so I'm not sure how that's happened, that's not the standard setup.
Is it that you configured the production branch to be 'master' when you initialised hg-flow? As I say, SourceTree should have initialised it to 'default' if you initialised hg-flow in it.
You can change which branch is which but you have to be quite careful to keep things consistent. You can edit the '.flow' file in the root of your repository, and the production branch is the line that says "master = blah" (I know, 'master' is confusing here - I wish they'd called it "production = blah"). Usually, that would say "master = default" for the standard hg-flow setup, but it can be different. Personally, I like to stick to the standard setup, it's simpler.
If you change it, you have to make sure that whatever you change it to is an existing branch, and is at the correct point in the history to reflect your production build. Then you can edit the .flow file, save and commit.
Unfortunately you also then have to switch to *every* open branch, make the same change to the .flow file, and save/commit. This is *vital*. If you don't do this, you could have an inconsistent hg-flow configuration depending on what branch you're currently on, which is a potential source of massive pain.
HTH!
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