Hi Jcb,
It sounds like you are artificially growing some trees, perhaps a new climate change strategy? :-)
Can I suggest you try this filter
-keep_class 5 - filtered_transform
That can work with a few types of filters but not all of them. I think it works with class and point_source filters. That should let you apply the change to your subset of points, and then still write the unaffected points out into the same output file as the affected points.
Regards
Sam