Clear Spotlight History
Settings > General > Spotlight Search > Check Messages > General
Go to Spotlight and do a search for anything that brings up old messages
Settings > General > Spotlight Search > Uncheck Messages > General
Go to Spotlight and do a search for anything that brings up old messages
Repeat this process until Messages IS checked in Spotlight Search settings but no old messages are found when doing a search.
The process can take as little as few times or up to several times. However, eventually the index will be reset.
I’ve tested this extensively and it works to clear Spotlight Cache of old deleted Messages.
iPhone 4S, iOS 6.1.2, Clear Cache Index