After multiple nightmares using Pr for HiDef, I had mostly wrestled a workflow out of it, even though it wasn't the most efficient and still had the occasional unpleasantness.
A while back, I had helped my wife and her friend shoot a single frame animation using different backgrounds to do multiple keys for the composite.
Today, we started a DV sequence, imported hundreds of *.tif files, stacked chroma keys on top of color keys, and repo'd tracks using the Replace with After Effects Composition all in the same stack. Made changes to some graphic background elements in Ps & imported them into Pr. Laid them into the timeline under the keys.
Exported an avi through AME.
Closed Ps, Ae then Pr.
Opened Pr and all the Linked Comps were there and timeline played fine.
Nothing crashed, glitched or got wonky along the way and I cranked out some complicated (OK, ILM I ain't) composites.