Does aeropress coffee change flavour after several hours? Every morning I make coffee with aeropress, fresh bean grounded with automatic burr grinder. When it is working day I would put it into a warm bottle and drink in office. I would arrive at office and drink the coffee around two hours. When it is holiday I would drink it immediately at home. Somehow I think the coffee taste not as good when I drink it in office. The coffee would have less acidity and a little more bitterness. I use a zojirushi warm bottle.
All coffee changes taste over time - it is full of relatively fragile organic compounds that will change over time. 

Even in a vacuum flask (without exposure to light), the coffee will keep chemically reacting with itself. There is also oxygen in the bottle which will aid the breakdown of various of the compounds.

There really is no way to perfectly preserve the taste of fresh coffee unfortunately!