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Are you saying the index editor does not open or it opens with nothing in it? Did you actually create anything in the default index?
The index editor opens with nothing in it. When I look in the project folder for the .hhk files I see the default index and another version marked .hhk_backup. When I open each with notepad the backup has the content and the other has just a few lines of information.
I should state that this project uses conditional text because I have two versions for two separate products. So, when I compile a source layout for either version and open the chm file, I see content from (let's say) version A index and keywords from the default index. The same occurs when I complile a source layout for version B. Again, I see keywords from index B and keywords from the default index. At this point, both indexes are OK, but I wnat to know what is happening with this default index.
Make a backup of your whole project before going any further. Then if anything here goes wrong, you are no worse off.
You say the content of that index is showing in the outputs you create even though that index is not selected. You should only see the content of one index so that problem is additional to the fact the default has no content. The latter should be fixed simply by deleting the default and renaming its backup, with the project closed.
The fact that you are seeing the content of two indexes, plus the fact that it is alway the correct one for the output and the default is curious. You never see both projects. I am wondering if when you created the new indexes, did you select the create copy option and therefore get the default keywords in at that point.
Alternatively, do you perhaps have the default keywords in the topics? Look at the meta tags in HTML (code) view.