Hi@FMELizard,
If you would like to keep cells intact, please ensure that "Expand Named Cells" in the reader is set to "No".This will preserve cells as insert points, and not explode the cells into their component geometries.For further information about this parameter please see : https://docs.safe.com/fme/html/FME_Desktop_Documentation/FME_ReadersWriters/igds/Cells.htm
In addition, this article may be helpful : https://knowledge.safe.com/articles/195/microstation-design-cells-and-fme.html