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Paratext by (190 points)

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The tools that we use for print (PTXPrint and Publishing Assistant are the main two) allow you to create rules to change markers. So, you could turn off all footnotes in the settings or delete a particular footnote with a rule.
by (8.5k points)
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Within Paratext, you could use \fe instead of \f for footnotes intended only for digital versions. You could then change all \fe to \f in your digital publication workflow and delete all \fe in your print workflow. Similarly, for \w you could use \wa.

Be sure to document (using a \rem in the FRT book, perhaps) your non-standard uses of these markers so that later users of your text can understand and benefit from your work.

by (598 points)
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I had similar thoughts to the other two answers here, but have a few additional comments.

1) If you only plan on stopping a few footnotes or glossary entries from being published, then semi-manually deleting at the time of publication is the best option. As @Phil_Leckrone said, many publishing tools include some way of creating "Changes", where you can give it a rule which it applies. This can include rules like "delete a footnote that starts with these certain words" or "delete the glossary entry with this particular term in it".

2) If you think there will be a lot of such footnotes/glossary entries, then it will be worth your time to set up using different markers to differentiate. But unlike what @LivingField said, I wouldn't recommend using a pre-existing maker incorrectly (like \fe). Rather I'd create a new marker in custom.sty which is named something like \zfapp or \zfprint or \z-f-app or the like (I can't remember off the top of my head if - is allowed in a marker name). Starting the name with \z is a great way of warning everyone that "this is a marker we're using in a non-standard way".

Then, when it comes time for print, you can simply set \TextProperties publishable or \TextProperties nonpublishable to get your desired results.

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