Why were the specifications of the Pipistrel Panthera downgraded?
This sounds like an overly optimistic marketing department which wanted to make the aircraft look better. Engineering would allow to predict top speed within a few percent, so I would blame neither the simulations nor the engine swap.

The web page for the Panthera lists 155 kts only for the maximum range condition, which makes sense. Propeller aircraft need to fly rather slowly to maximize range. The cruise speed with maximum power is still close to 200 kts.

Please consider that the required engine power of propeller aircraft grows with the third power of flight speed. To give you the 200 kts top speed, the plane would need to run the engine with 215% of the power setting (and fuel flow) needed for 155 kts.

Once you know the installed power, you get reasonably good results just with the zero-lift drag and the propeller efficiency when you use this formula:
$$v = \left(\frac{2\cdot P\cdot \eta_{Prop}}{\rho\cdot F_{ref}\cdot c_{D0}}\right)^{1/3}$$
Nomenclature:
$v\:\:\:\:\:\:\:\:\:\:$ speed in [m/s]
$P\:\:\:\:\:\:\:\:\:\:$installed Power [W]
$\eta_{Prop}\:\:$ Propeller efficiency; use 0.85 if not known
$\rho\:\:\:\:\:\:\:\:\:$ density of air [kg/m³]
$F_{ref}\:\:\:\:$ Reference area for coefficients, usually wing area [m²]
$c_{D0}\:\:\:\:\:$ zero-lift drag coefficient

The zero-lift drag coefficient for small propeller airplanes is around 0.02 to 0.025 if they have a retractable gear. A very well designed airplane might come down to 0.016, but that is already pushing it. To fly fast, a high wing loading is essential, and then the influence of all non-lifting components on the total drag is rather high. A well-designed airfoil might achieve a $c_{D0}$ of 0.0035, but the whole airplane will be closer to 0.02.

Things get even worse when you aim for higher flight Mach numbers. The Dornier 328 turboprop was initially calculated for 320 kts cruise speed, but Marketing felt the need to claim 340 kts. The difference does not sound substantial, but all engineers thought they must be crazy over in Marketing. In the end, the Do-328  needed 30% more installed power to fulfill the promises made by the (rather irresponsible) Marketing department. The increased engine power indirectly caused an accident in flight test when a propeller (with an unchanged, but now too weak propeller mount) broke off in sideslip and cut through 1/3 of the fuselage. Luckily, the aircraft landed without further incident after that ...

(Disclaimer: This is from the back of my head, and I think I remember the facts and figures correctly. If any of you know more, please edit the last paragraph!)