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This is a regression introduced by bug 353266, existing generated source folders are considered "stale" and removed during configuration update. Running project update multiple times results in configuration flipping between good and bad.
Fixed. http://git.eclipse.org/c/m2e/m2e-core.git/commit/?id=9a29b43091d60947277b2fa3f61ae17ecac06fcc https://github.com/sonatype/m2e-core-tests/commit/5f214f9940212474b6ea011c53a5920766737d4e
Moved to https://github.com/eclipse-m2e/m2e-core/issues/