This is simply a time-out error. It may disappear if you try again.
If you update one rule so that it now covers existing rules, then the existing rules are deleted. e.g. if you have 500 different IP addresses from google, and you update one of the rules to match all IP addresses, then the other 499 rules are not needed and will be deleted.
If you keep having timeout errors, you can try to run the SQL statement directly in MySQL. Here is the statement:
DELETE unknown
FROM `wt_site_access_rule` AS unknown
JOIN `wt_site_access_rule` AS known ON (unknown.user_agent_pattern LIKE known.user_agent_pattern)
WHERE unknown.rule='unknown' AND known.rule<>'unknown'
AND unknown.ip_address_start BETWEEN known.ip_address_start AND known.ip_address_end