The all-ones value is not just a "device didn't exist" case, it's also

potentially a quite valid value, so not restoring it would be wrong.

What *would* be interesting is to hear where the bad values came from in
the first place.  It sounds like the device state is saved after the PCI
bus controller in front of the device has been crapped on, resulting in the
PCI config cycles never reaching the device at all.

Something along this patch (together with suspend/resume debugging output)
migth help pinpoint it.  But it really sounds like something totally
brokenly turned off the PCI bridge (some ACPI shutdown crud?  I wouldn't be
entirely surprised)

Cc: Greg KH <greg@kroah.com>
Signed-off-by: Andrew Morton <akpm@linux-foundation.org>

drivers/pci/pci.c

@@ -848,6 +848,15 @@ int
 pci_save_state(struct pci_dev *dev)
 {
 	int i;
+	u32 val;
+
+	/* Unable to read PCI device/manufacturer state? Something is seriously wrong! */
+	if (pci_read_config_dword(dev, 0, &val) || val == 0xffffffff) {
+		printk("Broken read from PCI device %s\n", pci_name(dev));
+		WARN_ON(1);
+		return -1;
+	}
+
 	/* XXX: 100% dword access ok here? */
 	for (i = 0; i < 16; i++)
 		pci_read_config_dword(dev, i * 4,&dev->saved_config_space[i]);