Well, on the same network of branches as Colchester Town/St Botolphs, but renamed much more recently are: Frinton-on-Sea and Clacton-on-Sea (formerly without the "on-Sea"s), and Walton-on-the-Naze (formerly, curiously, as both the town as well as the naze itself have a "the" in their names, "Walton-on-Naze")
NXEA also renamed, again for reasons of sound common sense, a couple of stations
on the Crouch Valley (Southminster) line: "Woodham Ferrers" became "South Woodham Ferrers" (which makes sense, given that is where the station is, even if the town didn't exist when the station was opened, and so shared a name with a village further away), while "Fambridge" became "North Fambridge" - a very good move, as there is no place (nor now a bridge) called Fambridge, and a relatively substantial distance by road is necessary to cross the Crouch to get from North Fambridge, where the station is, to the entirely separate village of South Fambridge.
Apart from Colchester Town, I think all of these renamings took place in 2007/08 or so