I was running bitcoin core version 0.9 which accepted an invalid chain not adhering to the BIP66 protocol changes. This prompted me to upgrade immediately, however the new version is taking the already accepted blocks as already verified.
I suggest some kind of check to be made on the first run of the new version which checks if the version that was last used was one that did not adhere to some protocol changes, it would revalidate the last x-blocks on the disk.
Not a major issue, but could cause some minor problems in later forks.