Hi,
DFS Replication (DFS-R) uses staging folders to act as caches for new and changed files to be replicated from sending members to receiving members. The sending member begins staging a file when it receives a request from the receiving member. The process involves reading the file from the replicated folder and building a compressed representation of the file in the staging folder, this is the staged file.
After being constructed, the staged file is sent to the receiving member; if remote differential compression [RDC] is used, only a fraction of the staging file might be replicated. The receiving member downloads the data and builds the file in its staging folder.
After the file has completed downloading on the receiving member, DFS-R decompresses the file and installs it into the replicated folder.
I wouldn't delete anything until the DFS-R is fully healthy and functional, you can create diagnostic health reports to get more clues if you have any issues.
Best regards,
Leon