I have one BES for Domino version 4. I have only 230 users so I am using MSDE. I would like to do the following and am unsure if this will work. Here goes.

I would like to move my MSDE to another machine separate from my BES
I would like to setup a second BES (without the BES task running) replicating the BES folder but also pointing to this same MSDE inactively.
The idea is that if the primary BES fails, I can start the secondary BES and keep going invisible to the users.

Will this work?

It will work, but I wouldn't recommend it. It's a pain in the a... You have to do manually some things.
Change the server ID on the standby BES to the server ID of the primary BES, change the name in the host table of standby bes ... write me a PM with your mail address I will give you more details.

We do the same at the moment. We manually disable the BES services on the second backup server. It's a pain, and we're researching other solutions, but it works nonetheless.

Search for MSDE/SQL migrations on this forum. I did a writeup, as did a few other people, and could easily solve your problems there.

We tried the Domino clustering thing (as described in the BES tech article) under BES 2.2 but had too many problems with views in the state db getting currupted so we abandoned it. Now we are trying something using a 3rd party product to do data replication between the two servers.