Maizey, this isn't my bailiwick, so I strongly suggest that before you attempt to save or work on any important projects using that external HD, you speak to someone who is much more familiar with USBs, their idiosyncracies and related software utilities. Maybe contact the GAOTD member who runs this blog and ask him. Coincidentally, he's talking about USB's and syncing this week and offers a utilities comparison table. Click on his complete profile for the link the GAOTD police say I can't post here. :-)
UPDATE: I sent him a, er, um, singing telegram.
As much as I rag on MSFT for the way Gate's & Co have bungled security and failed to maintain standardization and ignored backward compatibility and used heavy-handed tactics to crush small developers, I want to think that if this USB device connectivity problem were really huge, there'd be a loud hue and cry. Instead, most people seem to be nonchalantly dashing between work, home, libraries, planes, clients and friends using all sorts of USB devices and I haven't seen a lot of press attention about failures to recognize drives. Maybe that's just because I haven't been looking, maybe it's because the problem only occurs with certain configurations or devices. I simply don't know at this point.
I presume that if you've installed something on the external in a way that literally registered it as "ON drive X" (or maybe created a shortcut on your PC to a folder "ON Drive X") and then the next time you plug it in, regardless the port, if the number of USB drives running is different and it's assigned Drive Y, maybe the shortcut wouldn't work, but the FOLDER would still be there. I look forward to learning right along with ya!