Seems there's a new bug in version 3.3.6. When selecting a file in the unstaged list it will not be moved to the staged list. Next time you try to select the unstaged file it will say that the file has been deleted.
Seriously, sourcetree is getting worse for every new release!
I have exactly the same problem and it can be solved by clicking on View -> Refresh after you do any kind of pull/commit/push action. But this is a serious pain of course.
I have both "Refresh" options checked in the settings but no joy....
I think this is the same as #1270390 . Hitting F5 is a workaround, but I agree it is a bug that is proving more annoying each day that goes by.
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