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SourceTree is Deleting Files when Staging Changes

HI all, recently I've been having an issue with SourceTree (on Windows) deleting files when I stage changes. It doesn't seem to happen with every file. Essentially, SourceTree shows the correct changes in the 'unstages' state. But when I click on 'Stage All' it seems to delete the file instead. I can't seem to post pictures, but below is a link to my StackOverflow description of the issue. Does anyone have any ideas what may be happening? Thanks in advance!

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