Very good question I think and lots of people will benefit from an answer.
What you need to remember is that accounts are only linked so long as they are authorised to be linked through Facebook. What you should do is maintain a second table of linked accounts in your database so that you know who is who and if they are linked with Facebook.
You should read this integration comment, it provides a lot of useful information.
http://crazyviraj.blogspot.com/2010/01/test-cases-for-basic-facebook-connect.html
It doesn't really say how to do things, but it makes sure you tick all the boxes of what you should be doing.
ie:
Sign Up should fail if the user denies
permission to the app (category: sign
up)
Since we need access to an email
address, Sign Up should fail if the
user provides publish permission but
denies email permission (category:
sign up)
If the user provides an email address
that already exists in your system,
fail Sign Up. Make sure no YouFace
backend tables are modified (category:
sign up, 1:1 mapping) PS - when this
happens, I didn't find a way for you
to de-authorize YouFace on the
Facebook user's behalf. The user must
manually do this if they wish you use
the same account but provide a
different email address.
Accounts created using Facebook
Connect should not be able to login
using YouFace's default email/password
login system (category: sign in,
account security). PS: Since YouFace
accounts require a password and those
created using Facebook Connect don't,
make sure to insert a random password
hash into your table to avoid silly
errors
Accounts created using YouFace should
be able to sign in without requiring
to be signed into Facebook, even if
when a link to a Facebook accounts
exists (category: sign in)
Any many more