Z390 Pro4 and USB internal headers

The connectors marked in blue are your USB 3.x ports, check to make sure there are
no bent over pins etc in them.
The connector marked in light brown is your front panel header (power, reset, LEDs).
Double check the pinout in your manual and make sure you have the polarities correct
on the LEDs. LEDs connected with the wrong polarity or to the wrong pins can cause
issues sometimes.

By the sound of it I would check your case front panel cables, there could be
a break or short/damage on them. It's not uncommon for these to get pinched and
short out or break inside the insulation where you can't see it.

Given the locations around the board it would be unlikely that he board is the
issue. You can check the traces going to and from the USB ports and effected headers.
It is possible some may have been cut/damaged with improper handling, it should
be pretty obvious with a magnifying glass. My first thought is the front panel
cables from the case however, they could have been pulled and come loose at the
ports or broken inside the insulation.

Good luck

Ah, I see what you are saying now. I believe some USB ports are provided by the
chipset and others are provided by a separate controller, Nuvoton I believe. If the
Nuvoton controller is damaged or dead that could be the cause behind your issue.
I think (can't say for sure as I can't read the model on the chip) it's the chip
next to the M.2 Wifi slot. You can check it for damage to the pins or the chip
itself.
The ports provided by the chipset shouldn't be effected at all so you still have
the option to use a USB hub if you need more ports, at worst, you can throw in
a PCIe x1 USB card.