Copying the model into an empty clean file should work. If not, there is definitely something in your file that is linked to those Layers.
Before resorting to the copy-paste into a new file exercise, you could try this:
1. Start a fresh file from "New and Reset".
2. Delete all Layers (except ArchiCAD Layer), all Sections and Elevations, all Layouts and Master Layouts (except 1 Layout and Master), all Materials, all Line Types, all Composites... you get the idea.
3. Save the file.
4. Open the problem file.
5. Delete the rogue Layers.
6. Merge in the saved empty fresh file.
7. Save the file.
See what that does.
David Larrew, AIA, GDLA, GSRC
Architectural Technology Specialist
a r c h i S O L U T I O N S
WIN7-10/ OSX 10.15.7
AC 5.1-25 USA