I downloaded the New International Biblical Commentary (NT-series). The books are available when I call them through my library, but Logos does not show them when I right-click on a Bible text and ask it to search for references for a specific text.
I assume you mean "Search for references to <NT reference>" eg. "Search for references to Matthew 2:1"
Do you get any results for bible in "Matt 2.1" in a Basic Search of the commentary (or with any other NT reference)?
Yet when I open a passage guide window with a reference that relates to either of these works, they do not show up in the window
I presume they do not appear as Commentaries in the first section of PG? Create a collection of your favourite commentaries and use that in PG ie. select Properties in the toolbar and select your collection from the Collection drop-down, so that it replaces the default "All unlocked commentaries".
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