Hi,
It won't make any difference for the PWM frequency, it'll be 5kHz in both cases except you can't really set PR2 to 63.5 so you won't get exactly 5kHz.

However, because the dutycycle is defined as the number of timer "ticks" the output is high in relation to the number of "ticks" it is low the prescaler setting also has an effect on the resolution because it makes the timer run slower so the total number of "ticks" in one period is lower.

So setting the dutycycle register to x won't give you the same dutycycle output if you switch prescaler setting. If you want the highest possible resolution you should use the lowest possible prescaler value.