Electric Make (eMake) emits this warning in v4.2.x when it reverts a job that made registry modifications (if --emake-pedantic mode is enabled).
Prior to ElectricAccelerator v4.3.0, eMake did not version registry operations the way it does filesystem operations. One consequence of this shortcoming is that when jobs that made registry modifications are reverted (for example, due to a conflict or an upstream error), the modifications made to the registry are not reverted. This can lead to inconsistencies between the registry and the filesystem, for example, if the job that was reverted was registering a TLB location; in turn, this can cause future builds to fail unexpectedly.
Prior to ElectricAccelerator v4.3.0, the best way to avoid this problem is to make sure you always have a good history when running multi-agent builds. By avoiding job reverts, you should avoid this problem entirely.