I put together a video to explain the process I use to edited my HDR time-lapeses. While this may not be the preferred method for yourself I've found it gives me great control over the images and colour and works well for me. Also I hope it helps you too.
1. Photomatix Pro
3. After Effects
Batch Render HDR bracketed photos in Photomatix Pro.
Output to 16 bit tiff files in a sequance.
Import all files into Lightroom for colour editing. (copy and paste desired settings to all frames)
Output images in another sequance to jpegs or tiffs
Import final sequance into After Effets (or any other program that takes image sequences)
Edit from here or render into quicktime Mov.
Edit Mov files in your preferred editing program.