I saw the same issue on a VMware NFS volume last week: dedup was already running 4 days, and had searched 5.4TB (volume is 800GB).
This volume used to take a couple of hours.
I ran a full deduplication, instead of a partial one, and after a couple of hours it had finished.
Now scheduled dedup runs like a charm again (couple of hours instead of 4+ days).
This is the command to run a full deduplication: sis start -s /vol/volume_name
During a deduplication run, it's normal to see a temporarily drop in free space.
This is because it creates a fingerprint database of all 4kb blocks, which it uses to search for duplicate blocks.
Regards,
Niek