I made a Weis beer and my primary fermentation temp was 19C. After 2 weeks I mixed priming sugar into my beer and bottled it. I then conditioned the bottles for a week at 21C. I know when in primary the fermentation temp is critical and higher or lower temps does have an effect on the flavour of the beer at the end. Does the fermentation that happens in the bottle while bottle conditioning to carbonate the beer have the same effect?
The simple answer is yes: the yeast will actively be fermenting in your bottle, which will contribute to the flavor. However, the effect on the overall flavor will be very very small. I've read that some commercial breweries actually bottle condition with different strains of yeast, so as not to allow harvesting of their proprietary strains that do the main fermenting.
As a side note, I always pour myself a little sampler when bottling (or, most often, kegging). That way I have an idea of what the beer tasted like before the final conditioning.
Yeah, I would say effectively "no" or at least not significantly (which isn't really different from djs' answer). Bottle conditioning is the same for various beer types, including beers that fermented at radically different temps (lager and saison, for example), so fermentation temps that have a huge impact on flavor do not carry over to bottle conditioning; that fermentation is over.