OK, it took me a while to decipher what your actual problem is (would’ve been easier if you described how to reproduce it, step by step).
But I think I can reproduce it (12.0.50):
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create a group track and an audio track, whose output you set to the new group track.
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select both the audio and the group track and do a right-click->duplicate tracks.
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If you now look at the output routing of the duplicated audio track, it is set to the duplicated group track. The actual audio routing though still goes through the original group, verifiable by hitting solo on the new audio track.
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If you now save the project and hit solo again, the output goes correctly to the duplicated track.
Yep, seems like a bug to me. You should tag your post with “issue” and open a call at Steinberg (won’t solve your problem, and no guarantee that it will be solved soon, but make them aware that the issue exists).
A workaround that doesn’t involve re-opening the project is just setting the output routing of the audio track manually to the duplicated group (just click on the group name again).
Anyone else can reproduce it and I’ll add it to the Issues Wiki…