In VinylMaster;
When you Vector the Shape, be sure and tick the Boxes as shown Circled in Red.
This will leave your new Vector Shape sitting squarely on top of your Bitmap Flower image.
" Menu> Order> To Back " will leave you in with something similar to Figure A.
Grab The Circle/ Ellipse Tool and create a Circle Directly over the center of your Flower. ( shown here in Yellow )
Select (click on) toy Raster (bitmap) Original Flower Line Drawing and Delete. This will leave you something like Figure B, here with Leaves Colored Yellow.
You can then send to your Plotter and Cut each Color Separately.
Pro Tip: If you would rather not Stack the 2 Layers (Single Layer Application),
Trim the one layer against the other (or Punch with a Duplicate) and add a Welded Stroke for Overlap.