need to manually update page numbers in indexes

My TOC is (and presumably other indexes I need to add will also be) all in order and appears correct, but the page numbers are the “absolute” page numbers, not accounting for the difference created by title page and indexes. I used to be able to edit them (but that was before the automatic hyperlinking was built in).

What is “the difference created by title page and indexes”? The rule of thumb is that if you need to edit ToC manually, it’s most probable that you don’t use the tool right: if you manage page numbers correctly throughout the document (using properties of page breaks if needed), then you will have correct data in ToC automatically. But to help you with that, more than what you wrote is needed.

There was never “before the automatic hyperlinking was built in”. “Hyperlinking” in ToC was there in LibreOffice (and OpenOffice.org) from the start (just tested now with OOo 1.0.3); and ToC was locked from edits since then, too. And it always was possible to edit the index and remove protection from manual changes … if you still want work hard to not allow software help you.

Do you want help with this, or is it just a complaint?

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