Generate from Major headings always worked for me.
First of all. The TOC tool generates a NCX, just to be clear.
From that, you can (optionally) generate an inline (HTML) TOC
If one of those exists (properly flagged), it will be replaced. If it does not exist (or not flagged) , One will be created and that operation WILL make the proper flags. (a dup TOC is an indication that it was not marked correctly)
Instead of deleting the NCX, Use the TOC tool to remove the current entries (recycle icon), then Generate from...
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