Are you using the 1_2″ version of the script from this article? https://creativepro.com/free-script-to-change-all-numbers-in-a-document-using-math.php

When you double-click the script, you should see a dialog box appear that looks like this:

Do you see that? Then select the “type” of number in the lower left corner (circled above).

In general, you do not need to do anything special with the script. Just double-click it and a dialog box appears. By default it adjust all the numbers (so sometimes you need to specify what kind of numbers you want to change). When you say it does not work, what happens?

Suzerp: It sounds like something is wrong, for sure. This doesn’t happen if you copy and paste from a new CC 2018 document to another CC 2018 document, right?

It shouldn’t be doing that. I wonder if you export the original INDD file as IDML and then open the IDML, is it still 3 column? If so, does it still turn to 1 column after copy and paste?

I wrote this up here:
https://creativepro.com/how-to-split-up-single-page-into-multipage-spread.php

You could enable the “Ignore Font Style Overrides” in the Define Preflight Profile dialog box. That way, bold and italic, etc., would not be caught.

But I think the best way to do it is to apply character styles to that text. See the three-step solution here:
https://creativepro.com/import-word-files-into-indesign-remove-local-formatting-but-keep-italics-and-bold.php

Yes, you should be able to use the Cross References feature for that: https://creativepro.com/tag/cross-references

In general, when you make changes to InDesign’s default preferences you should quit InDesign immediately, and then restart. InDesign only saves your preferences when you quit normally.

If you need to back up your preference files, this article shows where you can find them:
https://creativepro.com/rebuilding-indesign-preferences.php