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If you have a submodule and switch to a branch without the submodule, EGit destroys the submodule directory. Depending on your ui settings the deletion may happen without warning.
Patches: http://egit.eclipse.org/r/#change,4133 http://egit.eclipse.org/r/#change,4134
Changing to critical since work might get destroyed by this bug.
Fixed with 576abf64d138606814e4b67c8110c4ee1ae1b2ac in JGit and 118228576e64895a7a24e2c6bac7a5289ea86c10 in EGit.