I see. Interesting. Sounds like you already have a backup of your HD's, so thats good. Now you want to use winUAE to do the work that the Amiga used to do until you get the Amiga fixed..or replace it all together.
So now you want to format the HD with winUAE... no idea.
your Amiga it will not boot? Because it still easier to do what you want on an Amiga, since you not using your original HD, there is ZERO risk of loosing your data. Not to say that it impossible but some things are easy if you don't need to trick windows into doing something that it does not do at all. I would fix one problem at a time, first order get the 4000 into a working condition with a NEW hd and new os, otherwise it is just one huge mess.
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BTW the final goal of running the thing on winUAE may still be possible but I feel like you are skipping some steps and making this harder than it needs to be.
patients .. you will get this working