One blank line may or may not be a scene break depending on how the PML is layed out. There is no good automated way to determine if this should be a scene break in this case. The it is possible to profile and see if the document is separating paragrpahs with a blank line or not. However many comercial PML files I've seen have random blank lines between paragraphs simply because the conversion tool used wasn't very good or the author of the PML was just lazy.
The only way to do what you want is increase the number of blank lines for scene breaks in your document. Specifically calibre's PML input will treat two or more blank lines as a scene break.