When writing data to path "/" it is written only to default shard without affecting the others.

Picture this:
We want to replicate primary site to secondary. The primary contains data in 3 shards- topology, inventory and default.
Getting this state and writing it to the secondary datastore will write everything only to the default shard (even though there is data which should be written to different shards). 
Furthermore if the secondary datastore contained any data in those other shards, this data won't be overwritten. 

Committing WRITE transaction to the ROOT (path "/") should delete everything and then correctly write the data to the right shards. So that after the write succeeds the datastore only contains the written data.