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I have VIs (Kontakt) assigned to stereo audio tracks that I set to input for monitoring purposes. In the past, I could bounce to disk leaving those tracks on input and they would be included in the bounced mix. I reinstalled DP (in an effort to resolve an unrelated issue) and now those tracks are no longer included in the bounced mix. Am I missing some setting that enabled me to do that?

Yes but it’s hard to tell what from your description.

When I did something similar, I wound up deleting the instrument tracks and creating new ones. The MIDI was unchanged. I still don’t know exactly what I did and how but new tracks got me up and running and I’ve not seen this issue again.

Odd. If the monitoring tracks are assigned to the output you’re using for the bounce, it’s hard to know how they could be excluded.
I used this setup too, but I always print the VI tracks on the audio tracks used to monitor before the export, so this has never come up for me.

Well, I've solved my own issue. Under "Bounce Settings" there is the option: "Bounce includes Audio Patch Through". I'm guessing it got turned off when I reinstalled DP.