Remove ligatures from Document

Couldn't you use the Find/Change dialog for this? I guess it depends on how many documents you're working with, but I've done this in the past myself; I'd open a hundred small documents, set up a Find/Change query with "All Documents" selected in the Search: dropdown, then just click "Change All" and walk away from the machine for a few minutes. Make sure you untick both the "Ligatures" checkbox in Basic Character Formats and the "Discretionary Ligatures" in the OpenType Features. 

If that doesn't work for you, or if you are dead-set on JS: I went and found the first Google hit for "turn ligatures off in indesign with javascript" which was a thread located here, from 2009. It took me a few minutes to get it to work, but with a few minor changes, it seems to succesfully & silently turn off ligatures in all paragraph styles:

// Turn off all ligatures in all paragraph styles
// Originally posted to the Adobe User Forums by Kasyan Servetsky
// featuring Gabe Harbs suggesting "allParagraphStyles" way back in 2009
// and Joel Cherney adding a [i] in 2023


var myDoc = app.activeDocument;
var myParStyles = myDoc.allParagraphStyles;
for (i = 1; i < myParStyles.length; i++) {
    myParStyles[i].ligatures = false;
}

Hello @defaultr7v002let17e ,

Basically what you need is a script that goes through the styles and activates/deactivates the right properties.

.

Can you upload a sample in INDD/IDML with your current styles? If so, open a document and delete the content, leaving a few paragraphs applied, and then we'll be able to help you with your exact scenario.

There are probably all kinds of overrides in your documents, so the easiest and quickest method is probably to disable ligatures as a global local override (sounds like a contradiction in terms, but you get the picture) with this one-line script:

app.documents[0].stories.everyItem().ligatures = false;

If you have related paragraph styles you could change it with a click in your parent style. If not, you have learned to do it better in the future.