Many times I have a sourceTree window open on my repo, but I'm also making changes via git command line (git checkout foo, for example). I notice that when I do this, the sourceTree window is now out of sync with my repo state.
There should be no danger, except possibly in some cases where you initiate an action in SourceTree while it is out-of-sync.
You can tell SourceTree to refresh by using the F5 key. If you make a habit of doing this whenever you shift your own focus to the SourceTree window, you should be safe from any possible harm from using an out-of-sync UI.
I also think there is no danger. SourceTree is almost nothing but a graphical interface - the main work is done by underlying git. So even if SourceTree display is not uptodate and you trigger a git command via SourceTree the executing git process will take "the real situation" into consideration ....
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