This has been asked in the past with regard to a muktzeh key, and i was uncertain if it would be the same with something like a usb. If i have a keychain with a usb on it that i wear week round, come shabbos is it ok to wear it and only use the housekey? The usb is one of the flat variety, unobtrusive and plain black (although i doubt it matters).
It seems that the USB should be a Kli Shemelachto Lissur, which would be forbidden to move unless you would be using it for a permisible purpose, or you need it's place (It may be also muktza machmas chisaron kis because people don't use usb key-chains for other purposes).
However, http://www.revach.net/halacha/tshuvos/Shevet-HaKehosi-Key-Rings-on-Shabbos/2185 says that the Shevet Hakehosi says that all keys on a keychain are a single unit, and one would be allowed to keep a muktza key on a keychain. Therefore, the law by a USB should be the same.
One of the ground rules of muktzeh is that if you have a container with both muktzeh and non-muktzeh items, the container itself is not muktzeh.
Some have the custom of lighting shabbat candles only on a table with other things on it (such as food or silverware) so that the table itself can be moved on shabbat if necessary. See this halacha yomit for more sources.
It depends on the importance of the extra item on the key chain. It is not true that in all cases it is nullified to the other items.
For example a fob for your car with a large replacement cost would be in the category hasoren kis, the strongest mukzeh there is. And even a USB stick, though itself inexpensive, may enter this category if for example it is storing the only copy of important documents.
In any case, I believe most Rabbonim would say to have a separate key or at least separate it from the mukzeh before Shabbos.
If it comes up as an exigency in Shabbos, then if possible, it is best to ask your local Orthodox Rabbi about the specific situation. Any position taken by any answer here is going to be general and theoretical, at best. You have a specific case.
That said, and only for an exigency, for example in Shabbos someone discovers that they can't find their Shabbos key and this is the only one they have, and they are at home with no one to ask, and if it is an inexpensive usb stick of no special importance, then it might be correct that they could use the other keys for that instance.