The recommended approach here is to split the test assembly in two - one old with all the Fakes tests and one new with all JustMock tests. You can gradually migrate your tests from the former into the latter, or not at all. You'll then enable the JustMock profiler only for the latter test run and leave if off during the former.
We will investigate if there is a way to integrate JustMock and Fakes for a seamless experience, but I don't think this would be a priority for us, as JustMock and Fakes are not complementary products - you essentially use one or the other and never both within a single test project.
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