It's not that painful of a process. I've gone through it several times in the past. The biggest thing would be going through and changing all your accounts in Management Reporter to the new main segment number. Also, keep in mind any mappings for integrations that currently exist. For example, do you import your payroll or sales or anything similar from another source? If so, then those sources will most likely need to be updated with the new accounts.
As noted in Tristan's response, you can use the Account Changer tool in PSTL and do it through an import sheet that contains all the changes. This will change the account history and any reference to the original account throughout GP. Keep in mind that if you have any 3rd party products that the changer may or may not work with it.
I'd suggest doing this in a test company first. You could then create a copy of all of your MR reports and get them all updated and run comparisons to make sure everything is tieing out as they should be. You could also test out any imports that had to change as well and get a comfort level that everything is working. Running the process in the test company will also give you an idea of how long the process will take to convert everything. Depending on how many years of history you have and transaction volume, it could take quite awhile. I've seen it take over 72 hours but that was with about 12 years of history and not the speediest of servers.
Once satisfied you could then run the same process in the live company.
