Normally the Plesk control panel will not allow you to update the limits of a hosting account if the account is over quota. This can quite easily be achieved by altering the values stored in the database whilst updating the account.
Login to your Plesk server and connect to the MySQL server (psa database).
mysql -u admin -pcat /etc/psa/.psa.shadow psa
Once connected check (and keep) the current disk usage value (replace <DOMAINNAME>).
SELECT real_size FROM domains WHERE name='<DOMAINNAME>';
You will now see something similar to this - record the value given
+-----------+ | real_size | +-----------+ | 434324252 | +-----------+
Update the value to a lower amount which will allow you to update the limits within Plesk.
UPDATE domains SET real_size=0 WHERE name='<DOMAINNAME>';
Login to your Plesk control panel and update the account limits.
Once the limits have successfully been updated in Plesk you can restore the old disk usage value (replacing the number for the real_size with that shown in the SELECT query and again replacing <DOMAINNAME>).
UPDATE domains SET real_size=434324252 WHERE name='<DOMAINNAME>';
This completes the process and the Plesk control panel should now show the new Limits with the "over quota" disk usage shown correctly.