Even if files are present in Data-store, you can delete the data-store (VMFS File-system) on the LUN Device. I have attached step by step screenshots where i performed exactly the same activity on our environment. Here i had few unwanted files on the data-store which i wanted to decommission. Let me know if you can follow this without issues in your environment. - Thor.
Step 1:
Step 2:
Step 3:
Step 4:
Step 5:
Step 6:
Step 7:
Step 8:
