Please see this tutorial thread:
Resizing fonts and Changing Units per Em Values.
Probably, what you want to match are Caps Heights. Hinting won’t be preserved, but can be added again on export if you’re using a recent version of FontCreator. Composites will need to be recomposed and adjusted.
2048 funits / em is good for most fonts. 1000 is a legacy from fonts created for the MAC.