With USB flash drives becoming so large in capacity, it seems pretty simple to plug it in and leave it in while you do all of your work. The thing is, this was NEVER the intention, especially on a Windows machine, or when you use Microsoft Office. Safe to say any Microsoft program. The reason is due to the method in which files are read and then saved. Basically when you open a file directly from the flash drive, such as a word document, as you work on this file the 'auto save' feature within office will save your work to the same place it was opened from. This is all fine and good so long as you don't have a power failure or the USB device becomes unavailable. In this case you will find your data quite probably corrupted and even the office 'recovery' will not save the most recent, if anything at all.
A USB Flash drive was intended to save data for the purpose of taking it with you, plugging it in to another computer and transferring the file(s) to that computer. What you should be doing is just that.. saving the file to your documents (or your desktop if you do plan on simply moving it to your flash drive afterwards). Once you are finished with the document/file and have saved it to your documents (or desktop), you can then plug your USB flash drive in and copy/move the document to the device. Then when you move to a different workstation you can plug the device in, transfer the file across and then open it from where you copied it to. That way as you continue to use/edit the file, it will autosave as necessary, to the computers internal hard drive.
While I'm talking about the desktop, you really should use this as a work space just as you would your work desk. At the end of your work day, if you are a tidy person, you would clean up your current documents and file/folders and move them neatly to the side of your desk or better still, place them back in the file cabinet. Simply saving things to your desktop and then leaving them there is also a recipe for disaster. With Windows the 'shortcut' is typically represented by a small arrow stating it is a shortcut. This is important because you can safely delete this shortcut without deleting the document/program itself. Unfortunately for Windows, the default 'save location' is usually the desktop so it is no wonder your desktop becomes littered with icons. Saving files to the correct folder/library such as "documents", "pictures", "music" or "video" does actually make sense and if you really need quick access to the file then create a shortcut and place it on your desktop. Note when you plug in that USB Flash drive within Windows, you are usually greeted with a prompt asking you what do you want to do? and opening the file browser is one option. It is at that point where transferring (by dragging and dropping) your document to your desktop, will create a copy of (since it is on a different drive which is external, windows is smart enough to not simply move the file) so once this is done you can open from the desktop.
I have witnessed numerous problems when people plug that USB drive in and start opening word or excel documents directly from it, working away editing the document and then wondering why the file was all corrupted when they went to open it on a different computer later on. The reason would be due to the way it is being opened and saved over and over again within the office program. Do yourself a favour and save all the misery by teaching your brain to plug the drive in and then copy the file(s) you need over to the computer you are working on.