about problem number one:
As you report no issues with the boot SSD, and only a transient “disapearing” problem with the separate spinning HD, it may be a hardware issue. If you are still having the issue, please post the last few lines of dmesg soon after you observe the disappearing drive problem.
Use the following or something similar, this returns the last 20 lines of dmesg
$ dmesg | tail -n 20
Posting the result(s) of the following command (when the drives are working properly and when one drive has disappeared) might help troubleshoot as well
$ ls /dev | egrep “sd|nvme”
I am also using Gnome on my version of Ubuntu, but I never use Nautilus. You may also have luck on just switching to a terminal/bash for most file operations if the disappearing-drive issue is actually software not hardware, and if your problem is isolated to Nautilus.
about problem number two:
Because you note another issue with the spinning HD not being available from Jupyter until you open nautilus you may want to examine the following to see if there are any “missing entries” or unexpected options (note especially the “noauto” option that will stop devices from being mounted on boot)
$ cat /etc/fstab
$ man fstab
$ man mount
- Although it has been many years since I have edited /etc/fstab manually, knowing about fstab gives another search term for you to investigate (I particularly like the Arch Linux Wiki for all linux problems)
- Fstab configuration issues do not necessarily relate to the disappearing drive problem, but seems you have two separate problems going on (drive disappearing problem and drive not available until opened in nautilus)