We had the same issue, so I'll try to share my experience so far. It might be a bit long, but I hope it will be informative.
We have a catalog of self-development apps, including oracle decks, positive quotes and guided meditations. You can check our apps here: https://www.indie-goes.com
We created those apps in association with various authors from different countries. When we create an app of the same type (for example a new oracle deck), we do a completely different design (UI) but keep the same structure and navigation (UX), for consistency and not to reinvent the wheel every time.
So of course, we created an oracle cards engine, that we reuse for every deck. Same thing for guided meditations apps, which share a common engine (all those engines are hand-coded and we don't use external template generating services). In September, we began to see some of our apps rejected, because of the 4.3 policy. It felt like an earthquake, as it just jeopardized an activity we took years to build.
Despite all our pleas, Apple kept telling us we could not update our catalog anymore, and that we had to consolidate our apps. It was a low blow. Our first concern was to know how our authors would receive the news. We were fortunate to have understanding partners, who accepted to not have their own single app any longer, and to be part of a "portal" app containing all the decks.
But for software companies that work with less understanding clients (for example for those who offer their engines to brands, so they can create white label apps), it can be really catastrophic. Even if Apple's first motivation was to remove clutter from the store (which is a good thing), I think they decided to enforce this policy in a very brutal way. Frankly, our apps were absolutely not similar to all those Flappy Bird or Solitaire clones, which spam the store for keywords farming. They all had their own personality, targeted different audiences, and made sense from a customer point of view.
After insisting with Apple, we got in contact with one of their representatives. Our biggest concern was about customer transition from individual apps to a global app. To do that, we needed to update the code of our apps, so we implement some features that guarantee a smooth transition from one model to the other. We managed to negotiate with the Apple's representative the permission to make updates to our individual apps till the end of the year. After this deadline, all updates will be rejected again.
This is where we are right now. We are working hard on the new portal, which is regularly more complicated than expected: it's when you do things, that you realize all the difficulties this kind of transition can imply. Probably something Apple's executives will never realize.
Good luck with your projects!