I have two versions of PD installed. Editing the profile works for PD10, but with the other version the numbers get scrambled and the frame size will never be right. You should be Ok doing this.
Unless it is fast action or slowed down, you may be better off producing to 30 fps than 50 fps, if the custom profile doesn't work out for you. Played on computers it will make no difference, but played on televisions at 50 fps, it may be seen as PAL and may not play correctly. Just a guess.
Producing to a higher frame rate, PD will likely blend frames to make the extra frame needed to go from 48 to 50.
Last, try to use the same bitrate as the original, or slightly lower. Going higher does not increase the quality, but will make a bigger video file.
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CORNBLOSSOM