It's good practice to always commit any local changes before pulling (merging) new code. This is a bit safer if you are worried about conflicts really screwing things up, but generally, conflicts are just part of the process, so don't worry too much about them. You can resolve the conflicts on master, while still retaining the work on newwork without any conflicts. Then you can merge your branch back with (while still on master) git merge newwork. This creates a new branch, which will allow you to get your master up to date without conflicts, (checkout master again, then pull or fetch + merge). Is there a reason you don't want to commit those changes before merging? Generally that's the right thing to do.
The command as I know to re-apply the stash is git stash apply, though pop may be an alternative that I'm not aware of (or it could do something different, I don't know, so you probably want to use apply.) But they are still fixable, you won't actually fubar anything. Git stash is perfectly legitimate, though as Greg said, for some reason fixing the conflicts can get strange.
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