Some preferences are not system-wide but are stored along with the document -- ruler measurement units, for example.
The Preferences panel does not give any indication of which ones are system-wide or document specific; it seems you found one that is the latter.
You might want to put up a Feature Request for this: https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform
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In fact, very few prefs are application level and will affect exisiting documents.
Thanks for the clarification, folks. I posted a Feature Request for this option per your advice. Thanks so much.
Just what did you request?
I believe Jongware was suggesting an addition that would show which preferences are application general and which are document specific so you will iknow when changing if they will affect existing files, but I suspect you might be wanting to change the way prefs behave and have an option to make a change to what is now a document-level preference and have it apply retroactively the next time a file is opened.
I requested making that particular option a sytem-wide thing instead of a document-level preference.