The aliases SYNC_VAPP and SYNC_VAPP_CUSTOM_CONTENT seem to do similar things, this KB clarifies the actions each performs.
Virtual Appliance
To expand on the information available in the Available Aliases documentation:
vapp_sync -
This alias is used to push customizations from one node out to other nodes in the VAPP deployment.
vapp_sync will take the contents of the /Virtual Appliance/Custom/{application}/ from the VAPP node the alias is run on, and pushes to all other VAPP nodes. For example; if run from /opt/CA/VirtualAppliance/custom/IdentityManager/ it will push the /custom/IdentityManager/ folder contents to all other VAPP Identity Manager nodes.
sync_vapp_custom_content -
This alias can be used to gather customizations from across the VAPP Deployment and ensure the most current version is applied to all nodes. It will gather the contents of the /Virtual Appliance/custom/ folder from all nodes, compare the found files looking for the for the newest version of each and justifies /Virtual Appliance/custom/ on all nodes with the most current version of the customizations.