1. Disabled Quick Clip in Control Panel 2. Rebooted 3. Uninstalled it via App Manager 4. Rebooted 5. rm -rf'ed both $HOME/.quickclip and $HOME/MyDocs/Quick_Clip 6. Installed Quick Clip again using apt-get install this time (the original 0.3.1 -> 0.4.0 update I did via App Manager) 7. It appeared on the Status Bar after the installation was done 8. Rebooted anyway, as per the install message 9. It's still there, and working fine now (haven't exactly done any in-depth testing, but at first glance everything's showing up as it's supposed to)
chmod: /home/user/.quickclip/parent_files: No such file or directory