[USN Journal defragmentation]

Here is a post from another site that sums up the issue around deleting this file on a DC.

 

This can be a really BAD idea on a domain controller. If you delete this file it KILLS the File Replication Service that keeps multiple DCs in sync. After doing this you have to manually reconnect and reinitialise the NTFRS from a DC that is still working. If you do this on all your DCs (eg: both) the only supported way to get back to a working system is a complete domain reinstall (or backups).

 

 

So while it is normally safe to delete this file there is a ball buster waiting for you.

 

The source of that post is located here, just so you can see the post in context.

 

Sadly, I will say that a year or so ago I learned this lesson the hard way when I followed instructions from someone that sounded very competent and deleted the file from a DC.

[USN Journal defragmentation]

If you delete the $UsnJrnl:$J on a domain controller, you will create a big problem. Before recommending anyone deletes a system file, you should be very sure of what you are saying.

 

As far as I can find, there is no 100% safe way to deal with a fragmented UsnJrnl. In some cases you "may" be able to delete it with no significant side effects. In others it may be catastrophic.