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I honestly have no idea. If I was in your position I would probably just mod the original rom and not worry about the extra features. If you're lucky someone else may reply on here who knows more about the actual hex editing side of things. I know bits and bobs but nowhere near enough to know...
I'd imagine that it would have erased all the changes made to the rom. Unless you specifically knew how to repoint everything that was originally there as opposed to pasting over it. Everything that was there before would need to be added to free space on the rom, and then re-pointed. That...
Well the hacked engine removes all the scripts from the game so you can start fresh, but if you wanted to keep the original scripts and modify them yourself then I think you would have to stick to an original copy of Fire Red.
The hacked engine does provides lots of extra scripting options but...
I had that when I first booted it up. You need to make sure there is a warp pad in the place you want to come out as well as where you want to exit the current map, and that they are connected. This happened to me until I realized the I didn't have a warp for the exit in Pallet Town.
As for...
I have a weird problem that i've not heard anyone mention so far so it might be something i'm missing.
I've made a healing script as specified in the doc for the engine, when I die I end up in the right place at the pokemon center, but the first line of the healing text comes up on screen and...