One of the big reasons why I still use a secondary is that it allows me to crop higher quality yeast. The yeast cells that are still in suspension at racking time are the least flocculent cells, some of which may be petite mutants. Carrying these cells over to the next fermentation can have a negative effect on fermentation.
I have experienced exactly this problem with the least flocculent cells. I have found that after a few generations of harvested yeast, I sometimes wind up with batches that will not clear.
My SOP on harvesting is to swirl up the yeast from the primary and pour into sanitized containers.
No big deal, as they clear with time and gelatin, but sort of PITA. It lets me know when to get some fresh yeast.