At line 3747 of document.c the value of doc->priv->file_disk_status is set to FILE_OK immediately after it was set to FILE_CHANGED. This seems a bug, possible this glitch was earlier mentioned in the comments here. This information is needed to implement reload all, but disappears too early. (A similar field doc->changed nicely updates only when the text buffer is updated. It has another purpose, I know)
Studying the behavior in some more detail I wonder this enumeration type can be simplified:

typedef enum
{
	FILE_OK,
	FILE_CHANGED, /* also valid for deleted files */
	/* FILE_IGNORE -->  Not needed anymore? */
}
FileDiskStatus;

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