I am came across this problem, I am editing files in Premiere and I merge some clips just to have the audio synced with my footage (separete microphone) but when I import the sequence into Aftereffects the merged files simple do not get imported.
Sorry to hear about this. Let us know the version of Premiere Pro & After Effects that you are using. Are you importing the Premiere Pro project/sequence using File > Import command or are you using Replace With After Effects Composition command? Also, while importing are you getting any error codes or messages?
I am using the latest version of both softwares and no, I don't get any error messages when I do import my sequence from Premeire, all the files looks great and in order but the merged files form Premiere just not came with the rest of the files.
My work flow is - Merge the video footage with my separete audio file - edit what I need to edit and save the project. In After effects I am go to Import > Premeire Project - I choose the sequence and done. Again, everything oooks ngreat but no merged files.
Multcam works better and I can see the file on my After Effects timeline, however the audio file came unsynced to After Effects.
Merge files is problematic for a number of reasons.
Multicam works great. In fact, say you've got a bin with six different clips each with in-cam audio and a separate audio-only file. Simple select all, create multicam option ... and PrPro will create six different multicam 'clips' for you. Using the separate audio instead of camera audio.