So this might just be a problem with my order of operations. When I export .mov out of After Effects I always get a 1-2 frame blip somewhere in my file of my keyed footage going offline. it's a nice little easter egg I have to hunt for every video.
I merge my video and audio in premiere, cut to length then import the sequence to AE to key and apply graphics. Then when I export from AE if get the blips.
Please help me out, also is my workflow correct to cut merge in premiere import to AE then final touches back in premiere?
Quicktime usage is broken and additional bugs with teh AE cache may escalate the issue further. Make sure to clear the caches before rendering and ideally use image sequences. And yes, merging the audio before working in AE makes absolutely no sense, considering how limited its audio capabilities are to begin with. Cut the sequence, export the reference, key it, reimport the result in Premiere to repalce the clip then export the final output from there.
What, exact, version of After Effects are you using? Some versions handle QuickTime better than others.