If Data De-Duplication is disabled, the system files will remain and actually occupy a lot of space. Here is how to clear it:
The unoptimise command:
start-dedupjob -Volume <VolumeLetter> -Type Unoptimization
Check the status:
get-dedupjob
Clean up the Garbage:
start-dedupjob -Volume <VolumeLetter> -Type GarbageCollection