Problems selecting and deleting images

[Tenbob]

I am trying to edit a complex graphical document to reduce the file size. I want to delete multiple images but it seems impossible with the available tools in Nitro Pro. These are the problems I found.

(1) Editing doesn't work with layers. The original document has multiple layers. It would be easy if I could delete a layer completely. Or turn off visibility in some layers and edit the others. But Nitro Pro throws up a dialog that says editing doesn't work on a document with layers. You have to flatten the document to a single layer before you can edit anything.

(2) Marquee selects objects outside the marquee. I want to delete literally thousands of objects. You can select multiple objects with Shift+click. But this is impractical for the number of objects required. I just want to draw a marquee around them to select them all. But the marquee tool is impossible to use accurately. It seems to select any object that TOUCHES the marquee. I just want to select objects that are COMPLETELY INSIDE the marquee.

(3) Marquee selection doesn't work when one object is on top of another. I want to select several objects that are on top of other objects. I can't draw a marquee around them because dragging the cursor just moves the lower object instead creating a new marquee. You can only create a marquee if you start in a blank area where there is no other object.
I can't find a way to turn off this behaviour.

The combination of problems (2) and (3) makes it completely impossible to delete the required objects, even if I make repeated attempts using all the tools available.

Can anyone help with this, or is Nitro Pro not up to the job? I'm using version 11.0.3.173.