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Why does an additional repo clean the source directory

I'm using Bamboo remote agents.  My job checks out 2 repos.  The 1st repo is checked out properly and cloned into the checkout directory.  The 2d repo, which doesn't have a checkout directory provided, sees that the build dir isn't empty and then cleans the source directory along with the 1st repo checkout dir.  The 1st repo has 'Force Clean Build' checked, the 2d  repo doesn't have the Force clean option checked.

Additionally, I have 2 servers.  Server A has only 1 agent running while Server B has 5.  The build runs without incident on server A, but fails on server B.

Why does the 2D repo clean the source directory on server B?

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