You might use E-Calc to see the difference.
The two blade should be a bit more efficient.
A problem with E-Calc might be that the constant? for the three blade is not the same as your prop.
Where I'm at the three blade props are usually Master Airscrew, and the two blade props I use are APC E.
The Master Airscrew props were not specifically listed, so I ended up using the default constant.
12x6x3 seems to be the more common three blade size for my electric planes.
Since you didn't let any of the "magic smoke" out, you are likely OK.