It's not clear what you are actually attempting.
If your development board has a USB Bootloader, which it seems to from your description, then the application code must be written is a manner to always it to be relocated to correct position in Flash memory.
Otherwise, the application code could attempt to over write the bootloader.
What programming language are you using to write your application code, C or Assembly?
If C language, which compiler set are you utilizing?
Also, can you provide a link to your actual development board or upload the board's user manual?
BigDog