I just upgraded from 10.6.8 to 10.8.5. Started with a brand new SSD and did a full manual re-install of everything and moved settings over manually. Was quite painful. I felt it was important to do it, because I've auto-migrated to the last three computers and there was quite a bit of dead weight. As an example, my old setup had over 900 prefs files. The new setup, fully installed and running has less than 300…..
Anyway, I ran into a couple of problems when setting up DP. I worked my way through them, but I thought I'd share, in case anyone else runs into these issues.
Short version: Changing the names of the inputs in the MOTU PCI Audio Setup app using "Edit Channel Names" can break the L+R assignments in the Bundles window in DP when opening an old session. This means if you Edit the Channel Names, then open an old session that had different Channel Names, all the channels that have been renamed will not have their L+R assignments in place anymore, and you will have to manually reassign them.
If you have a lot of old sessions with complicated input setups like I do (I have 4 audio interfaces connected), you can imagine how problematic this is.
Long version: I have two 2408 interfaces in my setup. Since I was starting from scratch, I decided I would properly rename the MOTU 2408 channels. I've had my 2408's for almost ten years. Back when I got them, I started to rename them, but got lazy, and only renamed 5 of the 48 inputs, and then stopped. For the last 10 years, that's how it looked---5 custom names, and 43 generic MOTU names. Fine. Well, since I was starting fresh, I thought, ok, time to rename all 48 and do the setup correctly. I renamed all 48. When I opened my big orchestral template for the first time, I was checking everything, and I noticed in the Bundles Window that most of the audio input assignments were lost and had to be manually reassigned. You can see in the pic below, the first 5 channels have the proper assignments, but the rest is blank and they should not be blank. And at the top, you can see the custom names I gave: "2408-1:1, 2408-1:2, etc." Back 10 years ago, I used this naming scheme on those first 4 channels, and on this new setup, I simply continued it. I thought it was odd that only the first 5 channel assignments had survived. So, I started to wonder if the naming of the channels could actually affect DP's ability to remember the assignments.

So, I went back to the MOTU PCI Audio Setup app, and put back in the MOTU generic names that the DP session was used to seeing, and guess what…….ALL THE ASSIGNMENTS POPPED BACK TO LIFE! AHHH!!!! That's crazy!!

So, it appears changing channels names affects DP's ability to remember channel assignments. That's pretty terrible if you ask me. You would think that DP ignores a name that can be changed so easily, and instead actually looks for the hardware port.
I have a LOT of old DP sessions. This forces me to keep the old generic names. I can imagine someone who records a lot of live stuff and would want to change the names quite often would run into a lot of trouble when trying re-open sessions.
Anyway, I reported it to MOTU, but I just thought I'd let you guys know too. It's stuff like this that can trip you up, and it's hard to chase down.
Cheers.
-gabe