External SSD no longer bootable I have a Mac Mini (late 2014) with its stock internal drive and an external SSD via USB. The external drive has Sierra and this is what I always boot from. The internal is a clone of the external just for backup, cloned via SuperDuper.

According to https://support.apple.com/en-us/HT210190 I can update directly to Mojave on this Mac Mini. I downloaded the installer from the App Store and ran it to install on the external drive. It took about 25 minutes and gave a "success" message, prompting me to restart to finish. When I restarted, it booted from the internal drive instead. I went to the Startup Disk pref pane and made sure the external was selected and tried again. It booted again from the internal drive. Good thing I had it as a backup :)

In the Startup Disk pref pane, the external drive is selectable but it still shows as a Sierra boot. I can tell the install did write to the external drive but I suppose it didn't finish. I ran the installer again -- it only took a few minutes and again showed "success" and a restart prompt. Same result.

I cloned the working internal boot drive back to the previously-working external SSD. So in theory I would be back where I started, with the SSD running Sierra and being my boot drive. But it still won't boot into it and it still shows as a valid choice in the Startup Disk pref pane. I tried resetting the NVRAM but no luck. And holding option at boot does nothing -- yes, it's a wired keyboard ;)

Thoughts?
When upgrading from Sierra to High Sierra, the firmware on older Mac logic boards is also updated. This allows a Mac to boot the newer macOS versions (starting with High Sierra) from APFS container partitions. Sierra can not be installed to boot from a APFS container, but Sierra can recognize APFS and therefore allows the selection an APFS volume with Mojave as the startup disk. However, the firmware may not agree with the selection. Possible reasons for failure are given below.


The upgrade from Sierra to Mojave do not also update the firmware.
The firmware update did not occur because you used an external drive to upgrade macOS.


You could backup your important data to an external drive, then do a clean install of High Sierra to the internal drive. If High Sierra is not available, then select a newer version of macOS. Afterwards, you can do a clean install of Mojave to the external drive.

Update:

Back when High Sierra was first released, I remember many questions similar to your question were posted here a Ask Different. I believe the consensus was that the firmware can  only be upgraded from the internal drive. The update is written to the EFI partition on the drive before the firmware is instructed to update itself. The firmware is not capable of reading the update file from a USB drive. The firmware is capable of reading the update file from the first internal drive (disk0).