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.