When I first started out with a dual boot, it recognized it just fine. Konqueror was reading everything and I could play songs. Now that I have reinstalled, it is not really responding. The battery test button indicates that it is fully charged, however, when I try to play something, I get these amber lights blinking, most likely indicating that the "ipod software needs to be reinstalled", even though this is almost a brand-new ipod. I have not used it in a while. If there is any chance that the battery running dead causes files to be deleted, that could be an issue, though I doubt it. I have hardly even used it. This is all aside from the fact that My Computer is not recognizing it, even though it is showing up in /dev, and so forth. Whenever it is plugged in, the amber light keeps blinking, indicating that it is probably being used as a storage device. Any ideas? I think reading the material on it is just a matter of configuring (have no idea how to do that), but I'm not really sure what is causing its behavior when I try to play something on it.

dmesg says:

usbcore: registered new driver usbfs
usbcore: registered new driver hub
USB Universal Host Controller Interface driver v2.3
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt Link [LNKA] enabled at IRQ 12
PCI: setting IRQ 12 as level-triggered
ACPI: PCI Interrupt 0000:00:10.0[A] -> Link [LNKA] -> GSI 12 (level, low) -> IRQ 12
uhci_hcd 0000:00:10.0: UHCI Host Controller
uhci_hcd 0000:00:10.0: new USB bus registered, assigned bus number 1
uhci_hcd 0000:00:10.0: irq 12, io base 0x0000dc00
hub 1-0:1.0: USB hub found
hub 1-0:1.0: 2 ports detected
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt Link [LNKB] enabled at IRQ 11
PCI: setting IRQ 11 as level-triggered
ACPI: PCI Interrupt 0000:00:10.1[B] -> Link [LNKB] -> GSI 11 (level, low) -> IRQ 11
uhci_hcd 0000:00:10.1: UHCI Host Controller
uhci_hcd 0000:00:10.1: new USB bus registered, assigned bus number 2
uhci_hcd 0000:00:10.1: irq 11, io base 0x0000e000
hub 2-0:1.0: USB hub found
hub 2-0:1.0: 2 ports detected
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt Link [LNKC] enabled at IRQ 5
PCI: setting IRQ 5 as level-triggered
ACPI: PCI Interrupt 0000:00:10.2[C] -> Link [LNKC] -> GSI 5 (level, low) -> IRQ 5
uhci_hcd 0000:00:10.2: UHCI Host Controller
uhci_hcd 0000:00:10.2: new USB bus registered, assigned bus number 3
uhci_hcd 0000:00:10.2: irq 5, io base 0x0000e400
hub 3-0:1.0: USB hub found
hub 3-0:1.0: 2 ports detected
usb 1-1: new full speed USB device using uhci_hcd and address 2
NET: Registered protocol family 23
via_ircc: module not supported by Novell, setting U taint flag.
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt 0000:00:08.0[A] -> Link [LNKA] -> GSI 12 (level, low) -> IRQ 12
usb 1-1: configuration #1 chosen from 2 choices
via-rhine.c:v1.10-LK1.2.0-2.6 June-10-2004 Written by Donald Becker
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt 0000:00:12.0[A] -> Link [LNKA] -> GSI 12 (level, low) -> IRQ 12
eth0: VIA Rhine II at 0x1d000, 00:0a:e6:55:4d:c8, IRQ 12.
eth0: MII PHY found at address 1, status 0x786d advertising 05e1 Link 45e1.
via82xx: Assuming DXS channels with 48k fixed sample rate.
Please try dxs_support=5 option
and report if it works on your machine.
For more details, read ALSA-Configuration.txt.
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt 0000:00:11.5[C] -> Link [LNKC] -> GSI 5 (level, low) -> IRQ 5
PCI: Setting latency timer of device 0000:00:11.5 to 64
usb 1-2: new low speed USB device using uhci_hcd and address 3
8139too Fast Ethernet driver 0.9.27
ACPI: PCI Interrupt Link [LNKD] enabled at IRQ 11
ACPI: PCI Interrupt 0000:00:0b.0[A] -> Link [LNKD] -> GSI 11 (level, low) -> IRQ 11
eth1: RealTek RTL8139 at 0xd159af00, 00:30:bd:b5:21:47, IRQ 11
eth1: Identified 8139 chip type 'RTL-8100B/8139D'
ACPI-0212: *** Warning: Device is not power manageable
ACPI: PCI Interrupt 0000:00:10.3[D] -> Link [LNKD] -> GSI 11 (level, low) -> IRQ 11
ehci_hcd 0000:00:10.3: EHCI Host Controller
ehci_hcd 0000:00:10.3: new USB bus registered, assigned bus number 4
ehci_hcd 0000:00:10.3: irq 11, io mem 0xdffffe00
ehci_hcd 0000:00:10.3: USB 2.0 initialized, EHCI 1.00, driver 10 Dec 2004
hub 4-0:1.0: USB hub found
hub 4-0:1.0: 6 ports detected
usb 1-1: USB disconnect, address 2
ACPI: PCI Interrupt 0000:01:00.0[A] -> Link [LNKA] -> GSI 12 (level, low) -> IRQ 12
PCI: Unable to reserve mem region #2:8000000@d0000000 for device 0000:01:00.0
cannot request PCI regions
savagefb: probe of 0000:01:00.0 failed with error -16
savage4_smbus 0000:01:00.0: Using Savage4 at d1700000
usb 1-2: USB disconnect, address 3
usb 4-1: new high speed USB device using ehci_hcd and address 2
usb 4-1: configuration #1 chosen from 2 choices
usb 1-2: new low speed USB device using uhci_hcd and address 4
usbcore: registered new driver hiddev
input: USB HID v1.10 Mouse [Microsoft Basic Optical Mouse] on usb-0000:00:10.0-2
usbcore: registered new driver usbhid
drivers/usb/input/hid-core.c: v2.01:USB HID core driver
SCSI subsystem initialized
Initializing USB Mass Storage driver...
scsi0 : SCSI emulation for USB Mass Storage devices
usb-storage: device found at 2
usb-storage: waiting for device to settle before scanning
usbcore: registered new driver usb-storage
USB Mass Storage support registered.
bootsplash: status on console 0 changed to on
BIOS EDD facility v0.16 2004-Jun-25, 1 devices found
Vendor: Apple Model: iPod Rev: 2.70
Type: Direct-Access ANSI SCSI revision: 04
usb-storage: device scan complete
SCSI device sda: 1015040 512-byte hdwr sectors (520 MB)
sda: Write Protect is off
sda: Mode Sense: 64 00 00 08
sda: assuming drive cache: write through
SCSI device sda: 1015040 512-byte hdwr sectors (520 MB)
sda: Write Protect is off
sda: Mode Sense: 64 00 00 08
sda: assuming drive cache: write through
sda:
Attached scsi removable disk sda at scsi0, channel 0, id 0, lun 0
Attached scsi generic sg0 at scsi0, channel 0, id 0, lun 0, type 0
eth0: link up, 100Mbps, full-duplex, lpa 0x45E1
eth1: link down
NET: Registered protocol family 17
ACPI: Power Button (FF) [PWRF]
ACPI: Power Button (CM) [PWRB]
ACPI: Sleep Button (CM) [SLPB]
IA-32 Microcode Update Driver: v1.14 <tigran@veritas.com>
microcode: CPU0 updated from revision 0x3 to 0x5, date = 05082003
IA-32 Microcode Update Driver v1.14 unregistered
bootsplash: status on console 0 changed to on
powernow: This module only works with AMD K7 CPUs
eth0: no IPv6 routers present
eth1: no IPv6 routers present
bootsplash: status on console 0 changed to on
subfs 0.9
end_request: I/O error, dev fd0, sector 0
end_request: I/O error, dev fd0, sector 0
end_request: I/O error, dev fd0, sector 0
end_request: I/O error, dev fd0, sector 0
subfs: unsuccessful attempt to mount media (256)

No, dead battery cannot delete songs. If storing ipod for period of time without use, should be at 40% charge. If a lithium battery is discharged too low it will not be possible to recharge. Should not be a problem as the ipod will shut itself down when the cell reaches about 3Volts, but if stored at the minimum cutoff voltage for long period of time, that could cause a problem. Lithium cells only have a lifespan of 2-3years, before significant loss of capacity is noticable. I have not been very active with linux for last while due to new persuits and interests, but a search in the forums here will give you many threads on setting up ipods. I have even contributed to a few of those threads, but am getting rusty and don't have my ipods set up in linux at the moment so will let others answer the rest of your questions and don't forget the search function here, works great.

Edit: By the way, what blinking amber light? Is it the battery icon on the ipod?

I am getting some specialized assistance at ipodlinux.org. It turned out to be kind of a mess. I'm not really sure how it got that way, but things are under control.