Yes you can import xy centroid + bom and export centroid with part numbers.
Note: If you have an IPC Netlist file, you can just import that and FAB 3000 will automatically extract X,Y centroid plus part numbers. http://www.numericalinnovations.com/blogs/news/how-to-generate-a-centroid-file-aka-pick-and-place-for-any-pcb-in-less-than-2-minutes
1. Import xy centroid. Here's several tutorials showing how to import xy centroid:
2. Convert Centroid file to Component Layer. Go to menu: Assembly / Convert External Centroid (to Components)..
3. Import BOM. This tutorial should show all required steps to complete the process.
Note: Make sure to check the option "Merge BOM" during import. https://numericalinnovations.freshdesk.com/support/discussions/topics/14000015727
4. Merge BOM with existing components. If you haven't selected the option to Merge BOM (during BOM Import), go to the menu: Assembly / Merge External BOM..
5. Export Centroid file (menu: File / Export / Centroid...), and make sure to check the option to include "Part Number".
If you get stuck, feel free to send us your sample file and we'll be happy to create a tutorial movie.