Using the Windows PowerShell cmdlet, Disable-DedupVolume doesn’t actually disable deduplicaiton. Well…it sort of does….but it also doesn’t.
When you deduplicate a volume, the data attributes for the files are turned into ‘chunks’ and placed in the Chunk Store. Using the Disable-DedupVolume cmdlet doesn’t undo this process. It simply stops it from continuing. So deduplicated files will stay deduplicated but new files (or files that haven’t been dedupped yet) will remain in an unoptimized state.
To put the entire volume back in an unoptimized state, you would want to use the Start-DedupJob cmdlet and run a unoptimization job.