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I would create a separate Duplicate Sequence in PPRO with a new name.
This sequence will retain your multiple audio layers and you could copy them back to the D/Linked sequence ( if thats what you want).
I personally am no fan of DL between AEFX and PPRO. Too complicated and messy to manage and your question does nothing to convince me otherwise.
I am an INTERMEDATE proponent and I bang on endlessly suggesting this is a better /easier workflow.
If you had the time would you explain why you chose to use DL in your instance? (I am open minded)
When you use Dynamic Link to import an AE comp into PPro, the imported clip is a composite--both video and audio. Even if there is no audio in an imported comp, Dynamic Link will create an empty audio track--one of DL's quirks. As such, you don't directly have access to the individual video or audio footage items used in the AE comp when it's placed in a PPro timeline.
However, you can easily copy footage items--in your case, audio--from your AE comp's timeline and paste it into a PPro timeline, as described here. I'm assuming you have an animation timed to your audio track(s), and want to preserve that--no problem. Just copy the audio clips from the AE timeline, position the CTI at the same relative position in PPro, and paste. Your audio clips will be placed into as many tracks as are necessary (depending on any overlapping) and you'll have access to each individual audio clip in the PPro timeline.
shooternz -I haven't used After Effects or Premiere Pro very much - I'm just learning them. My workflow is to bring some 3d generated clips into After Effects to touch them up and sequence them. Previewing with sound files is a huge pain in AFX (unless I'm doing something wrong). Seems you have to RAM preview for sound to work, and if you shift anything around, you have to RAM preview / pre-render again each time.
Premiere Pro makes that previewing a snap, and also lets you adjust audio levels.
Using the Dynamic Link lets me go back and forth between the two programs in a trivial fashion so I can use the best part of each program.
Not sure what 'INTERMEDATE proponent' means - was that a typo for intermediate, or is there some other method of working between After Effects and Premiere. I'm also open minded, particularly since I'm too new to either program to have formed any particular bias, so if there's an easier way, I'd love to hear about it.
Thanks for the tip and the link. The copy and paste across programs worked fine. And yes, I had arranged my sounds on the AFX timeline and wanted to keep them in order for organizational purposes. (Didn't realize how easy it was to slide stuff around in Premiere Pro, however. Having seen / heard it, I'll try to do most of my sound arrangement in that program.
typo correction "intermediate"
Any sound work in AEFX is a PIA so you probably do have the correct workflow.
I bring the synch audio into AEFX if I am keying synch sound clips but I do not bother even trying to hear it there
I export audio with the clip back to PPRO (as an intermediate).
I would never bring in multiple audio tracks.
Off-topic, but like the "new look!"