How do you Batch Load image sequences

I understand that, but this is something of a workaround. I was suggesting that you move all of your images into one folder, perform the steps I mentioned, then go back into Explorer/Finder and Undo to get all the images into their respective folders.

I'll usually do this by going into the top-level folder with all of my image sequence folders, searching for .exr or whatever my format is, dragging those search results into a new folder, then doing what I suggested in AME. It's not ideal, but it does work.

Alternatively, you could batch load your sequences into After Effects by dragging all the folders into the Project panel.

If you have all of your images in the same folder and they all have different naming schemes (which seems likely) then you can do this. Select all of the images in the Import dialog, and the "[Format] File Sequence" checkbox you saw before turns into "Multiple Sequences." Check this box, then you'll be able to import multiple sequences in one go. After you your encoding is finished you can go back into Explorer or Finder and hit Undo a few times to move everything back to their respective folders.