I wish it were possible but as far as I know its not possible to store it in a separate file, so it does have to be maintained. In fact it could be very bad to lose the key on an upgrade because if you use encrypted or hashed passwords and that key changes I'm pretty sure it will lock out all the users and be difficult to recover because I'm pretty sure that key is used as part of the encryption or hashing.
What I would recommend is to keep a copy of it in a comment section within user.config so you always have a place to copy it from. Thats what I do on my site also with the system.net mailsettings section of Web.config. Keep it in comments in user.config then after upgrade I restore it to Web.config from there.