Save the eBook so you have it as is. Then do a regex search (check the dot all box on the Mode: line) for....
Code:
<h2>(.*)<h2>.<h3>(.*)<h3>
and replace with...
Then generate the ToC. Once that's done, copy the contents of the NCX ToC and close the eBook without saving it. Then edit the eBook again and paste the NCX you copied over the one that's there. Done.