Okay, great! I've had this issue before even when attaching Thunderbolt items to different machines: Macs, Hacks, Windows, etc. –It's a Thunderbolt memory problem. I'm assuming that you're not dual-booting your setup between Windows 10 and OS X. When your system/EFI is working, but the Apollo won't behave, do all of the following in sequence:
- Shut down the Apollo and then everything else.
- Shut down the computer all the way and flip off the power supply switch at the back of the PC.
- Disconnect the AC adapter from the back of the Mk II or unplug the adapter from the wall, etc.
- Flip the computer's power supply switch to Off to drain the power supply. It takes ~1 minute.
- Press the On switch on the PC to make sure it's really dead.
- Unplug all Thunderbolt cables from the Apollo.
- Unplug the Thunderbolt cables from the Z390 Designare.
- Let everything sit dead for 10 minutes. Do not repower anything yet.
- Reconnect the Thunderbolt cable to the computer first.
- Reconnect the Thunderbolt cable to the Apollo second.
- Reconnect the Thunderbolt cables and devices as needed.
- Flip the computer's power supply switch to On. But do not power it up yet.
- Reconnect the AC adapter to the Apollo and flip the power switch to On.
- Flip on everything else for your setup that's not the computer. Count to five.
- Press the power switch on the computer to power it up: F12 as needed.
You may have to press F12 to get the right boot device loading. This should do it if you've solved that earlier EFI issue. Please share your EFI w/o serials if you're really getting hotplug to work. I have the same setup, but mine is the Apollo 8 Quad, Thunderbolt 2. Let me know how it goes.