What format are the files you're trying to bring into AE? After you batch processed them they're no longer RAW correct? After Effects also has the ability to batch edit raw sequences, so you might try bringing them into AE and exporting them as a lossless image sequence (TIFF, PNG, whatever you like), then deflickering them in LR Timelapse. I've never used LR Timelapse, but once you deflicker them you have to export them again correct? What format are the files when you output them from LR Timelapse? Maybe LR Timelapse is giving you a problematic extension. Otherwise we need to know a lot more to help you. Please provide answers to the questions listed here: "FAQ: What information should I provide when asking a question on this forum?"
They are still pictures that were shot in RAW on a still camera. It calls them cr2 files in windows explorer. They are raw image files brought into bridge and when edited in camera raw-the metadata is saved to an xmp file that accompanies each image. Then you bring the images into LR timelapse and it just adjusts the xmp(metadata) files to deflicker them. Much in the same way that camera raw works. You do not have to export the still at all because all of these changes are saved in the metadata. Then you drop the still sequence into AE and export it as video. It just wont let me export them into cs6 with these xmp files.
The raw files are called cr2 files and without the xmp file-they will import into AE. I tried importing some other camera raw files (NEF files) into AE with the xmp's and it worked. For some reason it does not like these RAW cr2 files with the xmp metadata.
Thanks for your time and help,
Here's a link to the LR timelapse forum where someone else had a very similar problem. Maybe this will provide an answer or a workaround.