Policy 2 in the paper states:
A backup procedure cannot access any fossils. That is, it
must upload a chunk if it cannot find the chunk, even if
a corresponding fossil exists.
So the second backup will still upload a new chunk even if the same chunk has been turned into a fossil by the prune operation.
Moreover, Policy 3 guarantees that fossils collected won’t be deleted before the second backup is finished:
For each backup client, there is a new backup that was
not seen by the fossil collection step.
Of course, this assumes that the second backup is using a different snapshot id so it is counted a unique backup client.
This is not a bug. There is really no need to support multiple simultaneous backups with the same snapshot id. If that happens, then it is a configuration error.