+1 on the need to re-store the choices upon changing password and fixing the over-write password without asking bugs.
Some work-arounds to try....
@cobalstarr: Even if plug-in changes your password incorrectly for a site entry, the old password should still be in the password history, which is viewed by editing the site entry, then clicking the clock with CCW arrow on just above the right side of password field. Should help recover from over-written passwords.
@jim260: There are some tricks you can try to change behaviors with complex domain names that need different site records. Under My Vault > Account Settings (lower left) > URL rules, you can force domains to not be treated as equal based on host or URL prefix, see https://helpdesk.lastpass.com/account-s ... #URL+Rules