I upgraded my server from the last version of FTB Beta A to FTB Ultimate. After making sure to make a backup, I copied our world folder over to the new folder I made for the FTB Ultimate server. Then I made sure to copy the right settings into the server.properties file - the world name, especially, has to match the old server.properties, otherwise it will generate a new world. From there, there were nearly no issues, and upon connecting, I and my users noticed that performance jumped significantly - our server was getting 3 ticks per second on Beta A (ugh), and with Ultimate it moved it up to 12. That was definitely the most noticeable change.
Of the problems I had, the only pressing issue was one of previously placed BuildCraft conductive pipes not working properly - this almost caused a huge explosion in an array of steam boilers (and their engines) that one of my users had set up. Several of my own pipes exploded, but thankfully stopped there because I only use Forestry's electrical engines. I would recommend turning off any BuildCraft engines before upgrading and turning them back on one by one after verifying the connection works properly. In our case, we replaced everything with redstone conduit and the issue hasn't come back, but it's possible the BuildCraft conductive pipes work fine still.
Another thing to note is that mystcraft's format has changed and if you had a full notebook from the Beta A version of Mystcraft, that notebook will be nearly worthless - you'll have to collect those symbols again with the new system. Some users might be mildly upset by this if Mystcraft was important to them. Their old descriptive books and worlds will still be there as long as you copy the entire folder over, so it's not a huge issue.
Other than these 2 things, there's really no problems I've noticed as far as compatibility with everything that existed up to Beta A. With Ultimate, you will notice that there's new mods with new ores in the Worldgen. You won't have areas with the new ores until you generate new chunks. So, you'll have to explore a bit to get access to the new ores so you can craft the new things available to you. The same is true for the magic aura nodes from Thaumcraft - your areas that have already been generated will be devoid of magic nodes. A dedicated server admin (with way too much time on their hands) can build new nodes quickly from a newly generated area with nodes using creative mode and Silverleaf saplings, a Hoe of Growth, and a nice chunk of spare time. Or you could just tell your users to go to new areas if they want to have access to Thaumcraft Aura. It's easy enough to do it that way, too.
One more thing to remember (no matter which way you go) is to make sure if you changed the config files (meaning in the /config folder, not the server.properties, which I already mentioned) on the server in Beta A that you change the settings in the matching config files on the Ultimate server - making sure not to simply drag the old config files over, but using the config files included with Ultimate, as in a few instances the format of the config files changed.
Other than that, I can't think of anything you might want to look out for. It was nearly painless, and nearly trouble-free. The main problem I was concerned about was whether people's inventories and chests would carry over properly. I had absolutely no issues on that front. Neither did I have any issues with any placed blocks aside from the BuildCraft conductive pipes. All-in-all, I've probably only had to spend about 20 minutes in work to get the server in basically the same state as it had been on the Beta A pack - that includes connecting and noticing the BuildCraft pipe issue and stopping things from exploding.
No matter which route you go, be sure you back-up everything first. If you decide to go Ultimate, keep in mind what I said - your mileage may vary, of course. I cannot recommend Ultimate enough, though. It's a fantastic successor to the Beta A pack. It has all of the same mods that Beta A had as well as a few more to make the experience even more fun and interesting. I don't think any of the other FTB modpacks has all the same mods that Beta A has - I could be wrong, but if I'm not, Ultimate is your easiest bet in that department.
