I've created a bunch of animations in HD at 1080/29.97 only to find out they actually need the animations in 720/59.94. Can I just export these files in that format, or drop my 1080 comp it into a new comp in the 720 setting, or do I have to re-create everything in a new composition from scratch?
You could nest your original comp into a new comp with the correct settings, then right click on the precomp in the composition panel, select transform from the pop up menu and choose to fit the layer to the composition width (or height, whatever looks best). This will alter the scale property of the layer. You can manually alter the scale, but this way ensures you get it just right.