Yum metadata from unrelated folder incorrectly removed when regenerating a folder

I have two nexus repository (oss) servers, trying to host RPMs.  There seems to be an issue in generating the repodata, as most of the time, i only end up with a repomd.xml file, and none of the files referenced from within repomd.xml.  I've got this happening in two different servers, with similar, but unique RPMs.

The only unique thing we are doing is having multiple yum repositories (repodata's) in a single nexus repository.  So we would have centos/6/ and centos/7/ inside the same nexus repository.  Which should create (with repo depth of 2) centos/6/repodata/ and centos/7/repodata/.  

In the log files, there are no errors, just lines like this:

2018-08-31 21:00:17,412-0400 INFO [event-9-thread-474] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Rebuilding yum metadata for repository tempyum
2018-08-31 21:00:18,515-0400 INFO [event-9-thread-483] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Scheduling rebuild of yum metadata to start in 60 seconds
2018-08-31 21:00:20,507-0400 INFO [event-9-thread-474] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Finished rebuilding yum metadata for repository tempyum
2018-08-31 21:01:20,507-0400 INFO [event-9-thread-486] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Rebuilding yum metadata for repository tempyum
2018-08-31 21:01:26,006-0400 INFO [event-9-thread-486] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Finished rebuilding yum metadata for repository tempyum
2018-08-31 21:01:26,221-0400 INFO [event-9-thread-512] anonymous org.sonatype.nexus.repository.yum.internal.createrepo.CreateRepoFacetImpl - Scheduling rebuild of yum metadata to start in 60 seconds