When files are deleted they are usually still physically there, unless you have
wiped them with a special program that does it many times, re-writing and
deleting. I am a little confused from what you wrote. I think that you are
trying to re-use the flash drive which you expect to be empty, but it isn't as
far as Ubuntu is concerned. Is that correct?

If there are files on the flash that you want but can't access from Linux that
is another question. I am curious why this happened because I do this all of the
time and have never experienced it, which should not be interpreted as it can't
happen. I would like to know more. It seems that Ubuntu and Windows are not
reading the file table the same. What format are you using?

If you don't care about the files then you can simply re-format in either
Windows or Linux. If you want to format the drive in Linux you can do it from
gparted
which should be installed as the Gnome Partition Manager, under System
| Administration. I am in KDE at the moment so don't have the exact
wording. If it is not installed you can do it from Synaptic or from the
terminal as 'sudo apt-get install gparted'.

You can also format from the CLI, but it can be tricky unless you are well
versed in your device names. Here is a link:
http://ubuntuforums.org/showthread.php?t=282018