Are you using Fabric or not?
The data/cache is local cache and its safe to delete it before starting jboss fuse etc. You do not need to push any changes from data/cache to other servers etc.
The configuration is stored elsewhere such as in the etc directory and when using fabric then in the profiles, which is stored in git.
BTW, I'm not using Fabric. All bundles and their configurations are deployed/managed by maven and installed from a feature repository (also on maven/nexus).