Remember, the Mac creates a seperate trash (and desktop) folder for each disk.
Therefore when you put the files on that disk 'in the trash' you are actually putting them into a hidden trash folder on the flash disk. (Ditto, if you take a file from the flash disk and drop it on the desktop, you're actually moving it to the desktop folder of just that disk).
Therefore, to truly get rid of the files you have to empty the trash with the disk containing the files in use. Mount the flash card again, and see if the files are still 'in the trash' then empty it.