I have an ICY-box 4-bay external enclosure connected over USB 3.0 to my Debian home server which I use for backups. Whenever I reboot the server the hard drive bay is not detected at all. I can not find it in fdisk -l, and it doesn't show up in lsusb. If I power down the hard drive enclosure and power it up again, it is immediately detected and connects just fine. My other UBS devices (keyboard and UPS) show up just fine after reboot. Is this a problem with my hard drive enclosure or are there any troubleshooting steps I could do to try to fix this?

Unplug it, then replug it, if it shows up you need to figure a way to reread it when restarting.

Edit: You probably need to add it to your /etc/fstab file.

I currently have it in the fstab as:
UUID=[the uuid] /mount/location/ ext4 auto,rw,async,nofail,x-systemd.device-timeout=5 0 2

The problem is that the drive doesn't show up as a device at all so I can't even mount it manually. Currently I just restart the external enclosure, which I suppose should be the same as plugging it out and in again, although if that isn't the case it is most definitely something wrong with the enclosure. It is just very inconvenient to have to do this every time as I am currently sutdying abroad, so I have to instruct my family on what device to restart every time the server reboots (after a power outage for example).

Is there anything happening during boot that could possiby make the system completely ignore a USB device as if it wasn't even there?

I had a USB enclosure for a hard drive that worked without incident for years, until the drive passed away from old age, and never encountered anything like this.

That the device sometimes doesn't show makes me lean towards a hardware problem.

Have you tried changing out the USB cable for a known-good cable and plugging it into a different USB port? You might also try reseating the internal cable that connects the HDD to the enclosure.