From a Windows desktop to a Linux host has incorrect directory slashes
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deanhouseholder commented
When your VS Code is running on a Windows desktop, and you're connecting to a Linux host it fails to explore files and uploaded files have backslashes. So it creates a new directory on the linux host in the format of:
/home/user/code/project1\directory1\file1
This is obviously invalid so it doesn't save into the code project but instead creates:
project1\directory1
project1\directory1\file1
Slashes need to be reversed depending on target OS.