If I boot to Workbench I can see it in HDToolbox, but I still can't mount it or format it or do anything else with it.
If HDToolbox sees it then all else is a software problem.
Formatted the CF with the latest version of PFS
PFS-TD64, PFS-DS or PFS-AIO?
Is the CF card the only HDD in the A500? And in the A2000 was it the only HDD?
If there was another HDD in the A2000 with PFS, did you perhaps forget to store PFS on the new CF card?
Another thought, if you run HDToolbox on the A500, install drive, define new, read configuration, does it show exactly the same values as when you did the same on the A2000?
Did you successfully use CF cards >4GB before?