After seeing your post and having the same problem, I decided to see what I could do about it.
So I used the hack from forum.dailymobile.net/index.php?topic=54910 (I'd post a proper link but being a newbie I can't).
Then I copied the file from Z: to C: using ActiveFile and went to the destination list but no joy, it said that everything was protected and couldn't be edited. There were the Internet and WAP Services destinations in the list but no visible MMS destination. I turned the phone off and on again and things were still the same and I still wasn't allowed to add or edit anything.
So then I deleted the file on C:, turned the phone off and on again, and found the default access points off the SIM loaded into the default destinations and I was allowed to edit them. There was still no visible MMS destination yet the MMS messaging settings had the MMS access point from the SIM so we can conclude that this is by design or the default connection database is corrupt... (rant about Nokia here)
As my SIM doesn't come loaded with the correct APs I edited the Internet access point using the phone and edited the MMS access point using betalabs.nokia.com/apps/nokia-configuration-tool (reject the first dialog that appears and use the online editing in the Tools menu). You need to use the Configuration Tool because it can get at the MMS AP whereas the phone GUI can't because it's hidden.
I also found that a few other things were reset, including wi-fi discovery settings and Chat passwords. My e-mail notification also started working again.
Isn't it great that you have to root the phone to fix things that randomly break?