the patching system horizons has doesn't overwrite the old files, instead, i think they delete the old files and replace them with new ones, leaving the old files fragmented on your comp; so after those patches, if your comp is running a little slow, you need to defrag it
They actually put the new ones down, rename the old ones, unpack the new ones, delete the old ones, then delete any files that they don't recognize. So yeah, it does fragment you because of that delete step.