How to clear inventory stock present at different locations at one time.

You can use “Issue Inventory Part” to issue out inventory in different location within site. 

Do you mean that Move Inventory Part doesn’t do what you want?  Or you are meaning during the issue process you need to pull from multiple locations?

I Need to delete all the inventory at one time.

Then update the inventory with the accurate physical stock.

That will require a migration job to change the inventory to zero, then to increment the inventory to the correct level.  All items will have to be costed correctly prior to this evolution.  There isn’t another out of the box solution to do this within the UI.

You cannot delete the inventory but you can issue all out the stocks in different location using “Issue Inventory” 

Then once you have the accurate physical stock, received it back again using “Receive Inventory”

Another way I can think of is use “Inventory Counting”