Sorry for the delay!
We've seen this problem coming for a while, so I finally refactored the code so that non-instanciated points can also be removed.
I added a new method, Series.removePoint, that takes the point index as an argument.
See
http://jsfiddle.net/highcharts/yozwauke/ for demo.
The commit can be seen at
https://github.com/highslide-software/h ... bac81b7400, and you should be able to apply the patch directly to Highcharts 4.0.4/Highstock 2.0.4 using the instructions at
https://github.com/highslide-software/h ... pply-a-fix