After a day to contemplate the error of my ways, I set to removing the finish from the top of the arms in order to sand the scratches.  I spent some time trying to understand what had happened so I don't do it again.  I'm certain that the scratches were made when I was using the rasp to remove the slightly-proud finger joints on the arms and legs.  When ROS sanding afterwards, I didn't notice that I had missed the deep rasp scratches.  And, somehow I continued not to notice them all the way through applying the pre-color and 2C, which were both applied with scotchbrite pads, and I didn't feel the rough patches through the pads.  I only noticed after the 2C was buffed off.

My take-away is that when doing the final sanding, I need to turn off the shop lights and use a raking light across the surface to check for irregularities.  It's nothing I didn't already know to do, but I didn't think to do it this time. 

My repair started with scraping down to bare wood with a card scraper first.  Had I started directly with the ROS, I'm sure I would have had a lot of clogged sandpaper.   After sanding back to 180, I went through the same process as before - water pop, scuff with pad, vacuum, clean with mineral spirits, and finally apply the pre-color.   I did all this with one chair first to make sure I didn't run into any more issues.   After a successful application, I followed the same steps on the other chair.

As I was scraping, I took some photos of the scratches that became more evident once the surface finish was removed.   I'm really embarrassed by how bad they were. 

At least this one was somewhat symmetric.

One arm scraped and sanded.

I carefully applied the pre-color, working up to the edges of the sanded part without overlapping on to the finished sides.  I'm glad I decided to make the repair since it all went smoothly, but I would have preferred to avoid it entirely with better prep.

Once the pre-color is fully dried, I'll re-apply the 2C, and I'll be back on track.