I have not tried this but I think you are correct in concluding that they need to be in the same file.
When creating a hyperlinked BIMx file, ARCHICAD generates the 3D model, plus it generates the Layouts, plus it generates the Markers into the 3D Model that point to those Layouts. But with your current setup the 3D model and the Layouts are in 2 separate files so it cannot do that.
Loving Archicad since 1995 - Find Archicad Tips at x.com/laszlonagy
AMD Ryzen9 5900X CPU, 64 GB RAM 3600 MHz, Nvidia GTX 1060 6GB, 500 GB NVMe SSD
2x28" (2560x1440), Windows 10 PRO ENG, Ac20-Ac27