My guess is you can configure the USBFS component as a HID Bootloader in the "Bootloader" project and configure the USBFS component as USBUART in the "Bootloadable" project.
You need to invoke the bootloader project when you want to update the bootloadable project.
Is there some more details or a tutorial on something like this?
You can refer to AN73503 - USB HID Bootloader for PSoC® 3 and PSoC 5 to know how to use the USB HID bootloader.
An example USBUART project is available in creator. You can right-click on the USBUART component and open the example project.