@Lomkiri has it. Editing the TOC, does just that. The TOC (only).
I remove unwanted entries (raves, book lists...), but leave the content
Assuming that you have a file-per-chapter (TOC entry) construction.
View that chapter (you can use the existing TOC to get there if it still has the entry. The section (chapter file) is now highlighted in the book browser: right click on it: 'Delete'.
Calibre removes the TOC / NCX entry
What it does NOT do is renumber existing chapters.
(you could also just reposition the section in the list. That adjust the flow BUT NOT the TOC position. That will need an edit or rebuild)
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