Uncanny dodge should not alter flat-footed AC
As seen in stat-blocks such as the quickling, Uncanny Dodge does not alter the flat-footed AC stat, it merely prevents the character from being rendered flat-footed or from being caught out by invisible attackers. Other effects that deny a character their Dex to AC still apply as normal. Uncanny Dodge should have a change note for AC and CMD, and no other effect.