Since last summer, I’ve done several editing projects with Avid Express Pro using DVCPRO HD MXF files from p2 cards. The only way I found to export to After Effects, do my work, and then reimport to Avid with no noticable image change was to export my source shots as true, uncompressed HD. After doing my work in After Effects and rendering out my movie as an uncompressed quicktime, I would reimport into Avid with no image change.
For your case, I suggest you export your source shots as 720×480 quicktimes with compression set to “none.” Do your work in After Effects, and then render out your movie uncompressed. I think you’ll find that upon import, you’ll have no image loss.
p.s. Why do people always recommend using the Animation Codec for normal footage? It’s designed for animation, i.e., material with large, solid areas of color, you know, like animation is.