Clones are never a good thing, labeling them as okay just breeds complacency making the enterprise more enterprisey. It should be labeled what it is, a pile of tech debt. I'd almost list them as one of the greatest evils, because you need to maintain two separate systems dedicating engineering resources maintaining yet another system. The upfront cost of consolidating the systems will pay dividends in the future.

Understanding the level of effort to deprecate some of the clones you'll encounter it's reasonable to suggest that you're going to have to tolerate them but I would strive to look for opportunities to consolidate the clones.