This article is on how to remove a duplicate Line for the Same Location is Showing in AIC

First, verify first that the 2 locations are one and the same by trying to create a dummy invoice and add a stock to the invoice. If both changes, then they are one and the same. 

In order to remove one of the line, move first all of the quantities to a separate location, preferably one with no quantities in stock. (In the example shown in the picture above, we moved it to location S1) 

If there are any stocks attached to an invoice or multiple invoices, go to Sales History, check all the invoices with the quantities attached, and zero them out temporarily so  you can move the quantities to a different location. 

Next, once you have moved all the quantities in stock for the location which is showing up twice in the list, you can now delete one of the lines for the problematic location. 

After deleting the  duplicate line, move back all the quantities from the temporary location and then readjust all the invoices affected to reattach all the quantities.