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I noticed that when I delete a local repository by choosing Delete from the context menu when I select an existing repository, then choosing 'Delete Repositories on Disk' from the dialog, SourceTree removes my selected repository from the UI (which is good) and it deletes my files associated with the selected repository from disk (also good). However, it occasionally also deletes my first repository - and by first I mean least alphabetically.
As an example, I have 3 local repositories in SourceTree, 'A', 'B', and 'C'. Sometimes when I delete, say, repository 'C', SourceTree deletes 'C' but also deletes 'A'. The files associated with both repositories are moved to the Recycle Bin in Windows, and the local repositories are removed from SourceTree's list of local repositories. I slowly noticed my 'API' repositories disappearing from my machine over time, and finally figured out that this was happening.
If I choose to Delete a local repository and choose 'Remove Bookmarks' instead, SourceTree is deleting both 'C' and 'A' from the bookmark list (not expected), but leaves the files on my disk (as expected).
If repository 'A' has pending changes and I delete repository 'C', SourceTree will warn that repository 'A' has pending changes. If I cancel in the warning dialog, SourceTree deletes disk files for repository 'C', and removes both 'A' and 'C' from its list of local repositories. The files for 'A' do remain on the disk, but the connection to SourceTree is removed.
I am running SourceTree 3.3.9 for Windows.