they were smart they would have had two active enterprise distribution certificates. One for signing internal apps and one for signing external “research program” apps. That way when apple revoked their certificate, all there internal apps would not have been bomb’d.
It doesn't work that way. You can only have ONE iOS Distribution Certificate. They do have to be renewed yearly, but you have to revoke the old one in the process of creating the new one. (Or wait for it to expire.) I just recently did this.
Your apps on the App Store continue to work when you revoke the old one. But you cannot upload new apps signed with the old certificate. You need to re-build the app(s) and sign with the new certificate. So, the next time you update apps, you have to re-build with the new signature.
If APPLE revokes the certificate, it is a different story. They can revoke it in such a way that already-installed apps will cease to run.
For Google Play, it is a BIT different. You can have TWO certificates. The explicit purpose of having two, though, is to bridge the gap when renewing every year. It would be a mis-use to segregate apps between different signatures.
Having TWO Enterprise Programs would be a violation of the Enterprise Program rules, as well. It would of course be easy to accomplish through an affiliated company without disclosing the connection.
Whoever wrote about arbitrarily creating multiple distribution certificates at will doesn't know what they are talking about. Or, they are confusing them with Provisioning Profiles. a Provisioning Profile can be shared among apps, or you can create one for each app. But every Provisioning Profile has to be associated (for Distribution) with your one and only Distribution Certificate.
There are also Development Certificates. You can have many, but they are intended only for developer testing. Normally, each individual developer has their own. (Depends on company policy, though.) They give a scant few additional Super Cow Powers, there is no review, but they can ONLY be side-loaded by USB or WiFi with the device UDID enrolled first on the Apple Developer portal. You can enroll 1,000 devices of each type. (phone, tablet, tv, watch).
Finally, there is AdHoc Distribution. For normal Developer Program, this has the same 1,000 device limit. You can distribute internally/to others for testing purposes. Does not have any Super Cow Powers. AdHoc is also signed with your Distribution (not Developer) certificate.
(An example of a Super Cow Power is the ability to inspect an embedded uiWebView or wkWebView with desktop Safari.)