Hi there. I'm an Apollo 8 Quad/Pro Tools/Vienna Ensemble Pro user. I've been working on this hotswap issue for
months. Hot swap as in I can power-off the Apollo after quitting Pro Tools and later turn the Apollo back on and have it reconnect via the UAD driver/handler. I can save you some steps and grief: Thunderbolt Hotplug does not work for UAD devices and these
Z370 systems. I've used BIOS F5, F7, F9, and F11. Unless you are running Windows or a real Mac. In those cases, both ports work fine and you can flip power switches all day long and still regain your external Apollo. That's it. I have some great SSDTs that go into EFI<Clover<ACPI<Patched -and you can try them (my Thunderbolt card exists on RP21) -but I suspect that a result with an Asus Z370 with a Thunderbolt header and AIC will be the same as for mine (see build sig). FWIW, the SSDTs I use were originally built for X299 and Titan Ridge, but were rewritten to be used with the Z370 and the Alpine Ridge rev.2 -KGP wrote these.
I might be able to gain "hotswap" with a Z390 board, but I've decided that it's not worth the effort until I run this build into the ground. I just power-up the Apollo and let it fully settle before starting the computer. I hope this helps. I'm considering retasking this machine to run as a headless Vienna Ensemble Pro Server and just use one of my Mac Mini 6,2 units for Pro Tools and Apollo use.
Note that these are for my particular mobo and may require tweaking to work with your mobo:
Here's a link to a successful Gigabyte guide other stuff that you may find helpful:
Combined Effort...
Best of luck. LMK what happens.