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Headings & TOC

Headings and TOC entries are controlled by two independent style families. Consequently, TOC entries don't "pull the format from the sources".

Heading are identified as such where the are styles Heading 1 to Heading 10 (I'll use Heading n for short from now on). When the TOC is generated, text from Heading n is extracted to build a level-n entry which is styled Content n (n from 1 to 10, parallel to the heading level).

All you have to do to format your TOC is to customise Contents n styles.

Default font size

Since your text mixes Arabic and English, you have enabled Complex text layout in Tools>Options, Language Settings>Settings. Doing so gives access to a more complex Font tab in styles definitions. You can now define different default sizes for Western and CTL languages. If you want new defaults to apply everywhere, change Default Style. If you want your default to apply only to "common" text (i.e. excluding headings, indexes and TOC, headers, footers and other special-interest styles), customise only Text Body.

Unless you already have a very rigourous and consistent use of styles, change Default Style.

Document formatting

As Clear direct formatting messed up your present layout, this demonstrates that you manually formatted the whole document with buttons in the toolbar. This is the wrong way of doing it, all the more since your document is 200+ pages. As soon as a document has more than 5 pages and will be edited and revised before getting a "polished" version, usage of styles becomes mandatory (in my opinion). This is the only way to separate content from appearance.

Styles are kind-of semantic markup. You type your text without consideration for aspect, apart from giving paragraph the right style (and words or runs of characters a relevant character style). Then (or beforehand if you plan smartly your styles), you give styles distinctive attributes (font, size, weight, spacing, colour, indents, list decoration, breaks, etc.).

In a long, important, carefully written documents, only styles can facilitate the editing task; No direct formatting can be tolerated, otherwise style modifications won't propagate to text (direct formatting overrides style attributes and hides the underlying style!).

Even if you're in the last editing step of your document, it is still worth "styling" it all over. This can even uncover formatting mistakes. Once this is done, reformatting the whole document is only a matter of seconds, without the need to browse over all the text.