how do I refresh my wired ethernet connection from command line?

I'd use the nmcli commands for that purpose:

nmcli nm enable false && nmcli nm enable true

man page:

DESCRIPTION
       nmcli is a command‐line tool for controlling NetworkManager and report‐
       ing on its status.  It is not meant as a full replacement for nm‐applet
       or other similar clients but as a complementary utility to those pro‐
       grams.  The main usage for nmcli is on servers, headless machines or
       for power users who prefer the command line.

       [...]

  nm     NetworkManager
          Use this object to inquire and change state of NetworkManager.

         [...]

          enable [true|false]
                 Get networking‐enabled status or enable/disable network‐
                 ing by NetworkManager.  All interfaces managed by Net‐
                 workManager are deactivated when networking has been dis‐
                 abled.
                 Reference to D‐Bus:
                 interface: org.freedesktop.NetworkManager
                 method:    Enable
                 arguments: TRUE or FALSE

Please try:

sudo service network-manager restart

You could try ifdown and ifup to disable and then enable the interface. Assiming the name is eth0:

sudo ifdown eth0
sudo ifup eth0

If the problem is reassigning an IP to the interface and you don't want to bring it down completely, you can just request a new one with dhclient:

sudo dhclient eth0