Editing: I didn't read the full question and went to the problem. Apologies. Will attempt to help with the question.
For me, I have been fairly successful at fixing chip outs. First - disassemble. Next, use a small tipped glue tube or even a toothpick with a drop of CA on it. Place on the chipped spot. Either build it up or let a drop harden on the spot(s). After it hardens, put it on the lathe, take a scraper and sneak up on it to get it to near size. Sand the lumps to size with nothing less than 600 sandpaper with very light pressure. This might take a few minutes as you don't want to sand the good sections, only the high spots.
Prevention answer:
My guess is that you are using a mandrel and bushings for finishing. This is a recipe for chipping for many people. Thick CA finishes tend to chip more than light coats. I like thick finishes and as a result had the same problem on a regular basis you have, only I was having the problem on ebonies.
Besides lifting/chipping, when the bushings are "snapped" loose, or even "scored" with a skew point, the snapping tends to loosen or chip out the ends.
Are you finishing the ends of the blank - sanding the ends smooth and flat with tube? If not, and a piece is a little long and is pressed too hard to the fittings, chipping will take place.
Re-capping:
1. it occurs with thick finishes
2. it occurs when the bushings are snapped loose, even when scored.
3. it occurs when pressed fitted.
Cures:
1. thin finishes
2. bushingless during finishing (turning between centers/mandrel-less)
3. sand the ends smooth with the tube before assembly;
4. be careful in assembly and sneak up on the fitting.
