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Right now I'm using Wubi to install Xubuntu 12.04 on my 8GB flash drive, and I'd just like to make sure that when I boot from the USB it won't affect my hard drive's bootloader/partitions at all, and just keep it all on the USB.

Is this correct?

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The thing is right that It will not affect your hard drive partitions but you will get option for ubuntu in your Windows Boot loader. you will get entry for ubuntu on windows bootloader. When you will select it you must have attached your ubuntu installled USB drive, Otherwise It will show error.

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But I am not selecting to install Xubuntu on my hard disk, only on my flash drive. Will it not only use the bootloader on the USB drive if I boot from it? – Alex Aug 4 '12 at 11:01
Alex, you are running Dual boot with wubi. Wubi don't install Bootloader on your Drive but it modifies Windows boot loader and makes entry for Ubuntu. Don't worry. It will not harm to your windows boot loader and if any problem occurs I am here to help. – K.K Patel Aug 4 '12 at 11:07

I would advise you to do a full proper install to your USB and forget Wubi.
Wubi is for installing inside windows.

Installing Ubuntu to an external hard drive or USB memory stick is a very safe way to install Ubuntu. If you are worried about changes being made to your computer, this is the method for you. Your computer will remain unchanged and without the USB inserted, it will load your operating system as normal. When you connect and boot from the USB drive you will be given the choice to load Ubuntu or your usual operating system.

Have a look at this question for instructions on installing Ubuntu to USB drives, the process is almost identical for Xubuntu.

Can I install Ubuntu to my 32 GB USB pen drive?

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