The good folks in the eDir forum suggested I ask this here:

I had a NW5.1sp8 w/BM3.8sp4 server at a remote office.

I then installed a new NW6.5sp4a server in a new, separate tree, to
act as the BorderManager server (after I removed the BorderManager
from the NW5.1 server).

I then merged the two trees and re-established the legacy S2S VPN to
our main office. The problem is that I need to merge a secondary
replica with a Master. Here is what I now have:

TREENEW with a Master replica on Root partition and a Secondary on
..OLD partition.

Both are listed in DSREPAIR as ON.

So my tree looks like this:

---------many users
---------old NW5.1 server
---------Two test users
---------new NW6.5 BM server

My question:

After I do the partition merge can I move the BM server from O:.NEW to
O:.OLD then delete O:.NEW? There is nothing in O:.NEW I need to keep
except the BM-related objects.

Why or why not or how? Thanks!