--assume-unchanged is ignored in SourceTree (Windows 1.0.7.0) so I can't change branchs without issuing --no-assume-unchanged command then commit all (ignored) changes.
This is only an issue if the modified files in the working copy are also modified by switching branches. If that's the case you can use Stash, and you'll find that on the toolbar (the box).
You can stash your changes then checkout different branch. Not sure currelty stash is supported in SourceTree GUI, but definitely can use command line to do it.
http://git-scm.com/book/en/Git-Tools-Stashing
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