Hello,
What Database are you running? I believe you are running SQL database.
Yes you could delete the file in ....Program Files\Symantec\Symantec Endpoint Protection Manager\data\replication\outbox
This may contain huge data when there is a failure in replication.
I would suggest you to Restart SQL Server machine, clean %SEPM_Install_Path%\data\outbox\replication folder content on all SEPM, then run a new replication.
Reference: http://www.symantec.com/docs/TECH171225
Hope that helps!!