I had not been aware of any such problem, so tested it.
I located a Raw file that showed a fairly severe dose of chroatic aberration from a fisheye lens.
I removed the aberration in Lightroom successfully.
I then right-clicked on the image in the Develop Module and selected Edit in CS6. Selected "edit copy with Lightroom adjustments".
When the image opened in CS6, the chromatic aberration had not re-appeared. So, basically, I cannot replicate the problem you report.