Losing setting for content root when closing project

My content root setting changes keep being lost and reverted to the original settings when I close my project.
Is this an issue other people have had or is there something silly I may be using.

I simply go to
File
Settings
Directories
Delete the original content rootl
Add the new content root.
Click Apply
Click Save.

Howver whenever I close the project the settings are lost.

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