The logging out and in again trick worked again for me two times. Today I waited around 10 minutes and then logged out and in.
I also just created a bug report on bugzilla from Gnome: https://bugzilla.gnome.org/show_bug.cgi?id=773819 -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to nautilus in Ubuntu. https://bugs.launchpad.net/bugs/1633824 Title: nautilus ignores trash on external drives Status in Nautilus: Unknown Status in nautilus package in Ubuntu: Triaged Bug description: Using nautilus 3.20 as included in Ubuntu 16.10, I can move files to trash in general. However only the items removed from permanently installed drives shows up in the trash virtual folder. In the case of usb removable drives, the .Trash-1000 folder is correctly created, and the files are in there but the nautilus GUI does not show those files in its virtual trash folder. ProblemType: Bug DistroRelease: Ubuntu 16.10 Package: nautilus 1:3.20.3-1ubuntu3 ProcVersionSignature: Ubuntu 4.8.0-25.27-generic 4.8.1 Uname: Linux 4.8.0-25-generic x86_64 NonfreeKernelModules: nvidia_modeset nvidia ApportVersion: 2.20.3-0ubuntu8 Architecture: amd64 CurrentDesktop: Unity Date: Sun Oct 16 11:48:03 2016 InstallationDate: Installed on 2016-02-19 (239 days ago) InstallationMedia: Ubuntu 15.10 "Wily Werewolf" - Release amd64 (20151021) SourcePackage: nautilus UpgradeStatus: Upgraded to yakkety on 2016-10-13 (2 days ago) usr_lib_nautilus: gnome-terminal 3.20.2-1ubuntu5 To manage notifications about this bug go to: https://bugs.launchpad.net/nautilus/+bug/1633824/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp