I'd ask the question the other way around, rather than will Docker CE continue to share the Docker Enterprise codebase, it's whether Docker Enterprise will continue to share the upstream Docker CE / Moby codebase. They've always maintained an internal closed source fork for the Enterprise code, which has additional features. However, the development process of CE has always been open source, and features added to CE were mirrored from CE to the Enterprise codebase. The acquisition of Enterprise didn't change that it was already a fork of CE. And the acquisition did not include the CE code or any of the other open source projects, those continue to be managed by Docker, which they will maintain as a core component to their business (CE is embedded in the various Desktop products, and Hub has little value without it).
The biggest downside I see to the acquisition is the loss of staff from Docker to Mirantis. I'm sure many people had a dual role working on Enterprise and CE, and a significant chunk of the staff went to Mirantis. That said, the CE repos are open source, Mirantis staff can submit PR's for changes they'd like usptream, and they can pull down new releases of CE into the Enterprise product. The end result for users may end up looking identical to what we have today, just two close companies coordinating, rather than two sides of the same company. From an open source perspective, having more outside contributions is actually a good thing, since it forces governance and planning into the open, that in the past may have happened with internal meetings.
Disclaimer: I have been exposed to private discussions from the Captains program on this topic (not much since they are still working this out) and have done my best to keep my answer to only the public knowledge.