I had some big problems with upgrading my linux source node from 4.0.2 to 4.1.0. The policy on this linux source node is set to back up one set of folders under /opt/folder/. Immediately after upgrade, the node started backing up the entire system starting from the root directory and any subsequent fast resync resent almost everything. So it ended up bloating my repository and pretty near filling my disks. What I learned from support is that there is a bug in the linux software that will do this if you happen to have any exclusions in your policy, which I did. This is a known issue that the developers are working on for a new release very soon, so if you please be careful when updating linux source nodes. You should remove any exclusions as a workaround if you do upgrade.
The end result of this was that my store for that linux source node was hosed and to get it backing up properly again, I had to create a new storage group, and repointed the backups to the new empty store. Please post if you encountered this and let me know if there was a way to get the old store for that node back on track. I cannot seem to get the node to backup only the folder that I want anymore when it's pointed to that old store.