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This has been asked over email several times, so I'm documenting it here.
in how_to by (197k points)

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Keeping answer below for reference, but this can now be done without coding or manually modify Hyperlinks:


If you have the lightbox setting turned on, you can bypass it for individual links and have them open in a new window. To do so, you add a query string to the end of the URL in the Hyperlinks panel within InDesign. E.g.,

Starting Link (with no query string):


With added query string:


Starting Link (with existing query string):


With added query string:


Update (v2.6)

More on link control: https://ajarproductions.com/blog/2015/09/21/how-to-add-advanced-html-hyperlinking-with-in5/

by (197k points)
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Does &lightbox=1 allow me to do the opposite ? Most of my links shouldn't open in a lightbox, so I would uncheck the Lightbox in the in5 export, but then when I really need it, i would add it manually.
That's an interesting idea, Franck. However, if you don't turn on the lightbox option, in5 doesn't include the library in the output (to save file size in the output).

If it's just one or two items, you might want to create an MSO with an empty state and a lightbox state. Inside the lightbox state you could have a Web Content Overlay or Embedded HTML.
Has anyone got a neat script/find and replace recipe to change all links from watch to embed links? This is going to take me forever..