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Using the DB25 connectors to get 8 channels of analog I/O into the system will work just fine; yes, 4 stereo and 8 mono would be available combinations. Emote, the software that controls the H9000, can be used as a plug-in in Cubase to store your session settings; however, it is best practice to store the Session on H9000 as a backup.
Regarding I/O, the H9000 permits the simultaneous use of analog, digital, Dante, and Pro Tools. So it would be possible, for example, to get a Dante expansion card for both your H9000 and the Aurora for an extra 32 channels on top of your 8 analog I/O. Or, if you are on a Mac, you can connect the H9000 via USB to you computer and create what is called an aggregate device, allowing you to use the I/O on the Aurora in conjunction with the I/O on the H9000 as if it were a super interface; this is only possible on Mac, not PCs. This will give you 16 channels of I/O via USB into Cubase, plus whatever you have connected to your Lynx. From within your session, you can go direct to the H9000 without any conversion to the analog domain.