As long as you have a backup of your original files, you're good to overwrite the appropriate files as it is. No need to delete and copy everything, that would achieve nothing short of wear and tear on the NAND flash. If something's wrong or you want your old XMB back, just go back into recovery and copy the backup of the offending files back
-EDIT-
Figured you might wanna know that there's also a plugin that bypasses the need to replace files on your flash altogether named cxmb. Release thread is here. Simply shove it into the seplugins folder in the root of your memory stick, copy the files listed in that thread from your flash backup, and switch in any ones that you wish to replace. Personally, I still replace the files on my flash, but this way is far safer, albeit a tad slower due to reading from the memory stick.
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