The combination of settings is removing the binaries from the server and preventing download from Alliance.
Resolution
There are two options
Enable Alliance Sharing so binaries can be downloaded
In the UI navigate to Sharing Settings from the username drop-down
Check Enable Alliance Communication
Change the setting in cb.conf to keep all module files
Edit /etc/cb/cb.conf
Change KeepAllModuleFiles=0 to KeepAllModuleFiles=1
Additional Information
If option 2 was performed, binary files will have to be purged in order to avoid running out of disk space. See https://community.carbonblack.com/t5/Knowledge-Base/Modulestore-Filling-Disk-When-Alliance-Sharing-Is-Disabled/ta-p/43887