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Google does crawl JavaScript, and they do index it. Googlebot is really a form of the Chrome web browser, so they will see the information that you give to them and most likely the other remaining content. Keep in mind that cloaking is against their guidelines, so may get the site penalized.

I would go ahead and give Google and all visitors the full content.

usDragons, the best way to deal with these links is to use Google's Disavow Links tool to disavow them.

First, you need to identify all of the links, and you an do that by downloading all your links from Open Site Explorer, Majestic.com, ahrefs.com, and Google Search Console. Combine the lists and remove the duplicates.

You'll want to manually review all of them, make a list of the ones you want Google to ignore, then upload a list of the domain names using Google's disavow links tool. Google has more info about their disavow tool here: https://support.google.com/webmasters/answer/2648487?hl=en

They certainly will make note of those phone numbers, but since the phone number is not a web page there's no way to pass on "link juice" to it. So, there's really no reason to mark it as a nofollow link.

Whenever you migrate a domain name to another domain name (I think this is what you're saying you did), Google will keep the URLs of the old domain name in their index for at least a year. That's if you migrate to a new domain name.

If the pages have 301 redirects to other pages on the site or new pages on the site, then those old URLs could still remain in the index for a period of time--you'll be able to see them if you search for the URL.

Typically even if those URLs are still indexed, it shouldn't be hurting rankings at all.