Hi Graeme.
There's a few things that your describing, which really doesn't make sense from the functionality of NL.
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Install went fine, and unlike the USB thread, boots fine from HDD.
NL2 can see all 2TB of the drive.
Add a 3TB drive, and I had to re-enter the licence key and the activation code. Once I added the 3TB drive, both of these codes were returned to zeros - this despite the fact that I had already entered the code, and activated with the unlock code...
I'm assuming from the above, you installed NL to the 2TB, entered license, unlock etc. Then added your 3TB drive and rebooted, then had to renter your license ID, unlock etc, and NL didn't see your 3TB drive.
Based on my assumption of the above. NASLite has no ability to reset the license ID *at all* from just booting, it has no ability to do this *what so ever*. Unlock's will only fail from changes in major hardware such as a motherboard or ethernet card, NASLite does not check hard drives against unlocks, it simply doesn't do that. Even when a unlock is bad, it's not reset. the old one is still there in the menu until you enter a new one and save the config. I think this was addressed somewhat in another thread.
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So, no big deal - reenter and reboot. NL2 refuses to see the 3TB drive at all, and the HDT on the CD only sees the 3TB as a 700GB drive again - sound familiar?(rhetocial)
This is another thing thats puzzling, The Hardware Detection tool, isn't NL, it's a module of the syslinux boatloader, Linux and NL never boot when you access that. HDT gets the low level information about your hardware from the BIOS, stage 2 boot loader etc, and reports what the hardware says. NL's kernel after the initial boot would query the drive its self to get the information about the drive and populate the device tree, this is not something passed on from the boatloader.
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I would love to use NL2, but unless SE comes up with a bug-fix or other solution, I will have to look elsewhere, which would be a shame, as I love the simplicity of NL2.

This is pretty basic functionality and obviously something core to the product, and with 3TB drives being in the 130.00 USD ranged, I would expect more posts and support emails, which to date we haven't gotten any. If I have some spare time i'll do some testing with large drives and report back to either escalate this or close it out on our end.
Thanks.