QGIS » QGIS Application

1. Open an existing project file
2. Select Project -> Save As...
3. Save the project to a new project file
4. Select Project -> Save

What happens:
A warning dialog pops up telling me that the loaded project file on disk was changed and asking whether I want to overwrite the changes. The "last modification" date in the dialog corresponds with the save date of the original project.

What should happen:
The new project file created from the "Save As..." is overwritten without warnings, since this is the expected behavior of a "Save" operation.

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As far as I can tell, nothing bad happens if you select "OK" on the dialog (i.e. the original project file is not affected and the new project file is saved), but it is a disconcerting message. I suspect there must be a setting somewhere that tracks the save date of the project when it is first opened and this is not updated to reflect the new save date from the "Save As...", even though the user is technically working on a new project.