This is an unusual problem, and frankly it makes me a bit nervous. The fact that it stops working sporadically COULD indicate a problem with the connection as you suspect, but the fact that the file tree is still visible leads me to believe something more sinister is going on here. I first recommend you back up everything you can't lose to another drive. I realize you're talking about a lot of data, and trying to backup a failing drive can be very frustrating, but the suggestions I will make could (shouldn't, but might) cause data loss.
- Prevent further problems -
Because the file tree remains visible after the files have disappeared, I'm inclined to think the problem is either in the external drive's MFT or it is a paging/caching issue on the primary computer. The first thing I would do is ensure that this drive is not being used to store your pagefile:
1. Right-click "My Computer", select properties (or select "System" from the Control Panel)
2. Select "Advanced System Settings", then select the "Advanced" tab.
3. Under the "Performance" heading, select "Settings..."
4. Again, select the "Advanced" tab. Under the "Virtual memory" heading select "Change..."
5. Select your external volume's letter and select the "No Paging File" button.
6. You may need to restart your machine for the changes to take effect.
- Make sure it's not broken -
The next step would be to check the "disk integrity" (e.g. whether or not your drive is busted) with SeaGate's tools, aptly named "SeaTools." Follow the link below and be sure to select EXACTLY the correct product, then download and run the appropriate SeaTools to "verify disk" or "check disk integrity." I've not used SeaTools before so I can't provide you exact details. In most disk verification processes, the software must be downloaded and burned to CD, which you would then boot from to check the disk, but because this is a USB external drive, I don't know if that will be required. Either way, SeaGate's website seems relatively straightforward (once you've selected your device) and should be able to provide details. I should point out that you can expect a bit-by-bit inspection of a 2TB drive to take SEVERAL hours.
http://www.seagate.com/www/en-us/support/downloads/
- Defragment the Master File Table (MFT) -
If you still experience problems, I would recommend you defragment the MFT. This can likely be performed with the SeaTools you've already downloaded, otherwise you can use a third-party boot disc such as UBCD ( http://www.ultimatebootcd.com/ ), but a much simpler way would be to install the free Smart Defrag ( http://www.iobit.com/iobitsmartdefrag.html ) and schedule a boot-time defrag of the MFT. I realize this process may sound confusing but using Smart Defrag it should be quite straightforward.
- Ensure even power supply -
Still having problems? Check the power supply to the hard drive. Whether it's being supplied by the USB connection (which is unlikely for such a large drive) or a separate power cable, ensure it's not suffering from power sags by connecting it to a high-quality power regulator. If you don't want to spend a hundred dollars or more at least ensure you've got it connected to a high quality surge protector from limited help. This is the most likely problem if you receive a lot of popping in your speakers, or especially if your home suffers brownouts. Offering a more regular power supply to the drive may resolve these odd issues.
- Can't help much more -
At this point you've narrowed the problem down to a Windows setting, motherboard problem, or cable/connectivity issue. Try swapping the drive around to other computers to see if the problem persists. If not, try returning it to the original computer in a different USB port. If your hardware supports alternate connection types (such as FireWire or eSATA) you could also give those a try. Also, consider simply replacing the USB 3.0 cable with a new one, with data rates as high as USB3.0 it could be a small manufacturing defect.
Open the Windows Device Manager (open the Start Menu and type "Device Manager") and check for any items with a yellow circle containing an exclamation point over their icon: this is a device that's not working properly. Right-click on any faulty device and select "Update Driver Software..." to allow Windows 7 to search the internet for new drivers. If you find no faulty devices, go ahead and update the drivers for your motherboard, all of the "Universal Serial Bus Controllers", the external hard disk drive (identified by it's model name here, instead of it's volume letter), and anything else you think may be related to the issue. If all is as it should be NONE of these should have new drivers available.
Sorry this was so long, but faulty drives can be extremely difficult to diagnose. It's never a bad idea to include specs, thank you!