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I have a project, it is a Gradle project, and everytime I close Intellij it deletes the src files, they still exist in the directory just not in the idea project.

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I thing that is deal with IntelliJ cache. Try to refresh Gradle configuration. Open Gradle Tool Window and click refresh button .

I had the same issue with Maven and refreshing was helpful for me. Also may be useful system cache clean up.

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