How much relief is there in the neck now? You say it's an area in the middle of the neck that's the issue, suggests means there may be too much tension which is causing a concave bow, forcing the plastic up and out of their slots. Subsequent relief of the tension may mean they still sit proud.
No need to buy a new neck IMO. Have a tech shoot the fingerboard, or if you are confident in your skills buy the correct radius sanding block and do it yourself.
Hope you get it sorted!