Nope, there's no problem at all. In fact, if you set the bits in your code, you'll no longer need to set them in Picflash as they're now included in the .HEX file.

Try the above, a click on 'Reload HEX'. You'll see that the Oscillator bit have change to HS or INT RC... depending which code above you have used.

I also have that board. Can't live without now