Rhino keeps reference to deleted objects

Hi there,
I am stumped by a weird behavior in Rhino! I have a Rhino 7 model that apparently keeps a reference to some deleted/transformed geometry. I’ve deleted all “visible” geometry from the file, but when using a geometry pipeline in grasshopper I am able to see 928 objects (most of it duplicated geometry). There is nothing hidden or locked in the file and there aren’t any blocks. Anyone else who might have come across a similar issue? Is there another geometry concept other than locked, hidden and isolated that I might not be aware of?
The project I am working on is confidential so unfortunately I cannot share the file here.
Thank you!

not sure why that happens, but sometimes when I have a file that shows unexpected behavior, I can ‘fix’ it by importing the file into a fresh blank document and continue from there.
Confidential files can be sent to mcNeel directly for investigation. Rhino - Rhino Support