A minor glitch may be what is rendering the mounted APFS volume not showing up in Finder. Try rebooting your Mac and reconnecting your external drive after safely ejecting it.
If that doesn't help, consider accessing the drive from Disk Utility or Terminal to back up its data and then reformatting the volume.
① Open Disk Utility, right-click the APFS volume, and click "Show in Finder.
② Open Terminal, run the following command: (suppose the volume's name is Jenny's USB):
open /Volumes/Jenny\'s\ USB
After your data is backed up, open Disk Utility, select the APFS volume, and click the Erase button to format it.