Why did you remove files from the root/usr/lib folder using WinSCP?
A forum search turns up prior threads where updating the firmware via SSH is explained. Note most the directions are for v4.x firmware version My Clouds. The newer v2.x firmware My Cloud’s may use different commands to update the firmware via SSH.
https://community.wd.com/t/how-to-firmware-update-via-ssh/95476/2
#cd /shares/Public
#wget wget http://download.wdc.com/nas/sq-040103-421-20150217.deb.zip
#unzip sq-040103-421-20150217.deb.zip
#rm -f sq-040103-421-20150217.deb.zip
#/usr/local/sbin/updateFirmwareFromFile.sh /shares/Public/sq-040103-421-20150217.deb
Make sure to use the latest firmware name file.
One can find the links to the firmware in the following thread:
https://community.wd.com/t/wd-my-cloud-v4-x-and-v2-x-firmware-versions-download-links/148533
