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Disks added to running system not visible until reboot

aq flag

After my system has been running for a while, sometimes it stops responding to new media. I have an Icy Dock Black Vortex that allows hot-swapping of drives (each bay with its own SATA and power button). After dropping in a disk and pressing power on the bay, it lights up but fdisk never shows the drive. After I reboot, the hot-swap drives work correctly. Once the symptoms start, all new disks attached fail to work, whether it's an external drive, hot swap drive, USB drive, MicroSD drive, etc. dmesg shows nothing disk related after this starts. The CD/DVD/BD drive does still accept new media.

In this latest episode, the system had been up and running 36 hours. In the 12 hours prior, a few BDs were used, a MicroSD via a USB adapter, and then a hot-swap drive was powered on which never appeared. The duration for how long the system works properly before the symptoms start seems to vary considerably. Any ideas on what might be causing this, how to prevent it, or how to get it working again without rebooting?

This has happened to be as far back as Ubuntu 16 that I can remember, but currently on 20.04. I don't think I did much disk swapping before 16.

in flag
Silly question, but have you confirmed that "hot plugging" is supported by the motherboard? On workstation and server grade hardware, this is controlled 100% by the BIOS/UEFI configuration. Linux relies on the motherboard to do the preliminary lifting when swapping on SATA/SAS/SCSI interfaces.
aq flag
@matigo It does have hot plugging, they were all turned off. Weird because I can normally hot plug drives with it turned off. Let's see if it stops acting up with it turned on.
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