[slowsmile]

@AlanHK...

"I had a toc with 3 levels of headings, as mentioned. Using the plugin combined level 1 and level 2, deleted level 3. Only affecting the ncx file, to clarify, the HTML files aren't affected."
I draw the line at combining h1, h2 and h3 simply because I doubt many people will want to combine 3 headings per NCX heading. In other words your idea of combining 3 levels -- h1, h2 & h3 -- is unrealistic because I'm guessing that not many people will use it. More likely, they will prefer to combine just h1 & h2 headings in the NCX TOC. Add to this that such a plugin change -- to combine h1, separator, h2 & h3 -- would also make plugin usage more complicated. As I've already mentioned, I like to keep it simple for the user.

"Using Sigil's generate TOC tool gives 3 levels of headings.
Then using the plugin combines h1 and h2 text in the TOC, and the h3 heads disappear."
What you describe above is correct behaviour for the plugin because the plugin is only meant to combine just the h1 & h2 headings in the NCX TOC. The plugin does not combine or add h3. In other words, only combining h1 and h2 headings is what the plugin is supposed to do as is clearly stated in the plugin release notes -- it's certainly not a plugin error as you seem to be inferring.

"I know there is no formatting in the NCX, at least no way I know of."
Actually you can both generate and edit/change the headings in the NCX TOC quite easily in Sigil. Just click on Tools > Table of Contents > Generate Table of Contents or Edit Table of Contents and then right-click and edit each heading as you like. In this way you can edit/change each NCX heading in turn by manually typing in and adding h1, h2 headings with a separator and even, if you like, adding h3 headings appropriately to each NCX heading. And when your done, just press OK and your epub's NCX TOC will automatically update to your new NCX TOC heading format. And you could probably also use grep S&R within the toc.ncx file to achieve the same outcome or result.