what is your landesk patch level? Do you have mirroring enabled? There is a know issue with an old version and mirroring enabled.
I am on 9.5. Yes mirroring is enabled. It had been working fine (with Mirroring) until then. The night after when replication ran again, it had reversed the damage it had done and put all the data back on the Preferred Servers.
Happened again last night
I recommend you upgrade to SP2. There was a component patch LD95-CP_BASE-2013-0228 which addressed Mirroring within Replication process. This patch is available for 9.5 prior to Service Pack 1. Check out LDMS 9.5 Sustaining Patch Information, for other issues addressed since 9.5 release -
We have been SP2 for a good few months now.
on a pps check the folder "sdmcache", it should contain all the hard links to your replicated files if it is on the same drive as the share.
take a look here: How to check if the hard links in Content Replication are working
If your share and "sdmcache" folder are not on the same drive, try moving sdmcache on pps
(you will need to change this reg key: HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Intel\LANDesk\LDWM\Distribution\Multicast\Cache Directory )