This warning popup appears after a second click on Save as PDF.
Go to 'File/Preferences/Paths'
What is the directory for your patterns?
What is the directory for your layouts?
We'll need to know what operating system/flavor of linux (example: Ubuntu 16.10, Fedora 25 Workstation). Also the version of Valentina (from Help/About).
And please upload the pattern file (.val) and if you're using a measurement file please post the .vit or .vst. file. Tell us which item you tried to remove.
Does this error occur when you remove a particular item, or when you remove any* item?