Short answer - don't.
...may work one or the other time, with the restrictions you found and FLH3 mentioned. But more important is that this is very likely to cause Project corruption. Corruption as in 'f*cked up beyond repair'-corruption. It's a long standing problem and I won't try this until Apple themselves declare it fixed, which they haven't for more than a decade.
However - since this is somehow tied to the audio engine, you can disable Core Audio, open several Projects, do your stuff (compare / copy things, or work on external MIDI tracks), close all but one Project and enable CA again. This may or may not suit your workflow.