Can you post a new dmesg and lsblk?
After you upgrade under Windows, the Vendor ID and Product ID are change.
As I can see, you upgraded only one of the two controller from Windows (changed Product and Vendor ID from Western Digital to JMicron).
The default is Western Digital (I don’t know why, when it’s a JMicron product).
You have to upgrade under Windows the second one to get the same Product and Vendor ID (to rewrite them).
Finally, you have to change these IDs in this file: /lib/udev/rules.d/60-persistent-storage.rules
For more information check out: https://wiki.radxa.com/Dual_Quad_SATA_HAT#OpenMediaVault
Check out my last post in this thread for more information: https://forum.radxa.com/t/sata2-and-sata4-ports-not-working/5826/14