Another option is, after cleaning u-boot and fsl-image-*** using cleansstate command,
bitbake -c cleansstate u-boot
bitbake -c cleanssate fsl-image-***
1-) bitbake u-boot -c patch
2-) go to folder build_t1040d4rdb/tmp/work/t1040d4rdb-fsl-linux/u-boot-qoriq/2016.09+fslgit-r0/git
3-) copy source code to somewhere else to keep original source code
4-) then again in build_t1040d4rdb/tmp/work/t1040d4rdb-fsl-linux/u-boot-qoriq/2016.09+fslgit-r0/git folder, make your changes
5-) then write a patch for your changes using diff -u -r ORIGINAL_SOURCE_CODE_FOLDER MODIFIED_SOURCE_CODE_FOLDER > my_changes.patch
6-) then add this my_changes.patch file to your bitbake(.bb) file about U-boot which is under sources/meta-freescale/recipes-bsp/u-boot/u-boot-qoriq.****.bb or .bbappend
7-) The .patch file you created should be in sources/meta-freescale/recipes-bsp/u-boot/files folder
you can add this patch using SRC_URI = "<URL OF U-BOOT> / file://my_changes.patch". <URL OF U-BOOT> should already be written before. You only add this patch file on it.
Example SRC_URI:
SRC_URI = "git://git.freescale.com/ppc/sdk/u-boot.git;branch=${SRCBRANCH} \
file://my_changes.patch
Then again each time when you cleanssate u-boot and repatch it, all the changes should be made by default.