You could copy the relevant prefs.js items manually.
mail.account.*
mail.accountmanager.*
mail.identity.*
mail.server.*
mail.smtpserver.*
mail.smtpservers
For example:
egrep 'user_pref\("mail\.(account(manager)?|identity|(smtp)?servers?)[."]' \
< old-profile/prefs.js >> new-profile/prefs.js