The foliage tool has numerous instabilities that seem to occur randomly. One known issue is that painting foliage on other foliage can disable itself for unknown reasons. This can be fixed by re-applying the static mesh in that foliage actor. This seems to point to an updating error within the foliage tool. Another randomly occurring issue is that a foliage actor disappears from the listed foliage icons in the editor UI but is actually still there. To fix this that foliage actor needs to be deleted in the content browser and reapplied. You will loose any paint settings for that tool unfortunately.
This brings me to a suggestion: It would be nice to be able to duplicate paint settings from one foliage actor to another.