Retaining Bounding Box after Fishnet Clip

I have a large image that contains around 7000 trees.

I created a bounding box around each one of them and then saved it as a .xml file. I would now like to create different fishnet sizes and clip both the image and bounding boxes associated with the trees in that image. I know that I can simply make a fishnet and clip within QGIS, but I am not sure how to link the bounding boxes? Perhaps turning them into a .csv file with their xmin, xmax, ymin, ymax, classname and then clipping that with the fishnet?

Any other suggestions that I could consider? Would this be better to code?