These certainly need to be done carefully, otherwise the program could end up unusable and need to be reinstalled - hence the need to make a backup copy of the files before making any changes, so that they can be restored to their original state in the event of problems. I don't know if Amazon will do anything regarding this, as the emphasis now seems to be very much on Kindlegen.
I posted the information as I thought it might help some people. Googling this issue brought up loads of sites where people have hit problems when installing IE9. That was how I first found out about it, and initially reverted to IE8. I noted too that some people seemed to need IE9 for other reasons, so that going back to IE8 wasn't possible for them.
Creator is perhaps getting long in the tooth and maybe it is time to move on to other options. But for taking something from Project Gutenberg and producing a more user friendly book in regard to the navigation its not a bad tool. I use it for that and converting word documents for use on my Kindle/PC Kindle.
Were you able to make the changes to at least get the Guide option working?