So, from the ground up...
So the company owns >95% of the intellectual property rights. That's because the employer owns the copyright works created by an employee, unless there are alternative arrangement in place. It's another thing if the employee did not do the work "during the course of their employment".
The Git Repo is going to tell the company who wrote what. What was contributed by the employees will be there in black and white. Line by line.
The company could then:
- redevelop the <5% remaining sections of the code (which is GPL licensed) internally by its employees (during the course of their employment) or contractors who assign copyright in their work to the employer company.
- They could then licence the entire package on different terms - without the permission of the other contributors. Why? There's no GPL code in it.
- That assumes that the <5% aren't willing to assign their copyright to the company, so that they can deal with the copyright as it wishes to as the copyright owner. That could be done with a contributor agreement, or even a one line assignment, supported by consideration, "I hereby assign any copyright I may own in [code base name] to [employer name]".
Moving on to the Split.
So, it mostly depends on the state of the GPL'd code base when it was split between the older community edition and the newer commercial version.
What the company can't do is "unlicence" the versions previously released. See first sentence of section 2 of the GPL (v3). That doesn't mean that the employer must continue to make modified versions available for download.
The condition (section 5, GPL) is:
You may convey a work based on the Program ... in the form of source code under the
terms of section 4, provided that you also meet all of these conditions:
When you convey the work (ie make it available to others), you must convey all of it. But you don't have to convey it at all.
1. if the newer commercial version, only available to paying customers only has non-GPL software in it, it should be kosher for proprietary licensing.
2. there's no reason why they would need to keep conveying a code base to the community at large which does not have GPL licensed code in it.
BTW, there are specific tests to be applied (which are qualitative tests) to determine whether joint ownership of copyright exists in a single copyright work. As said above, joint ownership has different consequences in different countries. In the UK, any joint owner of copyright can prevent any other joint owner from exercising any of the exclusive rights of copyright - ie licence it or continue to licence software under the GPL.