Did the, almost, same thing.
Added msn protocol and naturally it imported all my msn-contact to phone book.

I found it looked way too cluttered having both names and a bunch of email adresses in my contact list.
When deleting an msn-contact it showed the warning which some seems to not read, "will delete from server too, sure??"

So what I did was uninstall the msn (haze) protocol thinking that would rid all connections to my msn-contact and it would be impossible for n900 to delete my contacts from server.
After that I went ahead and deleted all msn-contacts from my phonebook (although it still gave the same warning message).
Smart huh?

Naah... Somehow it still removed all my msn-contacts from the server.
And as the thread starter and many more I have contacts from several years back, even though occasional contacts, still important contacts.

Intensely unsatisfying result.

I remembered that I had some time ago seen a list of contacts sorted in different categories under some preferences tab in aMSN.
So I installed, logged in -> preferences.
And there you go.
They were all there, just that now they weren't on my list anymore.
Seems they somehow are still stored as contacts on the server.
So I added them all back to my list and yes indeed, they are all back.

Happy ending (TM)