It appears to me that these replication packages are created and left in AGOL when there is a failure in the synchronization, can anyone confirm this? At least that is one way they are created. There were a bunch created in our AGOL account this weekend (in our primary admin account's root folder), and when I checked our Portal logs there were various synchronization failures. Each failure correspond to a replication package on AGOL. I'm guessing in our case it might be a network problem because the layer being synched is not being actively updated -- it is a test layer. But the sync continues to run every hour. The replication packages don't appear to be created when a sync is successful.
I assume it is safe to delete these, as long as a successful sync happens after the last failure? In our case, we have had multiple successful syncs after the last error.
Here are some of the error messages I saw in Portal log viewer (bi-directional collaboration is set up and the errors reflect this):
The downloading of peer replication package on portal with id '{ID}' failed.
A scheduled job synchronizing items of collaboration '{collaboration}', '{ID}' and collaboration workspace '{ID}' with participant '{ID}' has failed.
The import of replication package on portal with id '{ID}' failed.