The only thing I can think of is that the item's setup on the general tab is marked as non-stock item so receipts or issues are not changing the item and maybe someone did a physical inventory and changed the quanity on hand to show an amount.  Read a couple of knowledgebase articles to see what you think.  I'm not certain it can be undone or corrected without a file fix from Sage.

https://support1.na.sage.com/selfservice/viewdocument.do?noCount=true&externalId=108832&sliceId=1&isLoadPublishedVer=&docType=kc&docTypeID=DT_Article&stateId=25352&cmd=displayKC&dialogID=1114401&ViewedDocsListHelper=com.kanisa.apps.common.BaseViewedDocsListHelperImpl&openedFromSearchResults=true

and

https://support1.na.sage.com/selfservice/viewdocument.do?noCount=true&externalId=108832&sliceId=1&isLoadPublishedVer=&docType=kc&docTypeID=DT_Article&stateId=25158&cmd=displayKC&dialogID=1134570&ViewedDocsListHelper=com.kanisa.apps.common.BaseViewedDocsListHelperImpl&openedFromSearchResults=true

The problem I have is the quantity on hand for an item does not show up in any location and the non-stock item box is not checked.   How was this received in without a location and how do I correct it?

A couple of ideas:  Can you find a PO that ordered and received the item?  If so, to what location was the item ordered?

In IV - File - Company Settings, do you show a default Location?

No, the default stock location is just a black box. 

Changes in Windows operating systems resulted in some fields appearing blacked out in Purchasing.

Resolution

Left mouse click inside the Default Stock Location box and drag across the text while holding the left mouse button down to highlight the text to make it visible.

Or Click the down arrow to the right of the Default Stock Location. The selected Default Stock Location will be highlighted. (Click cancel to avoid making unintended changes to the setup)

Changes in Windows operating systems resulted in some fields appearing blacked out in Purchasing.

Resolution

Left mouse click inside the Default Stock Location box and drag across the text while holding the left mouse button down to highlight the text to make it visible.

Or Click the down arrow to the right of the Default Stock Location. The selected Default Stock Location will be highlighted. (Click cancel to avoid making unintended changes to the setup)

It shows 01 as the default stock location.   However, when you look up the item and look at qty's in that location it does not show any on hand. 

That would be the default if someone didn't use a location on the PO.  I'd guess the PO may have been entered with an invalid location, (not sure it would let you do that, but it's worth a shot) so look for the PO.  I think under Inquiry - Item - you can see PO's.  Then open PO and go through each PO to see what location was used.

Okay I see that the item was stock receipt to location 903S but when you look at the location 903S there is no qty on hand for this item nor does it show stock transferred out. 

There was another forum question that said qty on hand could be out of balance with the location.  See:  https://www.sagecity.com/us/sage_construction_and_real_estate/f/sage-300-construction-and-real-estate/164250/inventory-stock-issue-posting/422727

It does give some idea as to why you might see this, and they did find a solution to fix it.

 How can I tell if there are reserved quantities?

In IV - Inquiry - Items, you right click and choose Show Columns.  Pick the Qty Reserved box.  I think this also shows on the Item's Setup and in Tasks - Enter Stock issues.  In Enter Stock issues if a batch has the status of Reserved, any items in that batch should show a quantity Reserved.   A few years back, you could accidentally delete a batch of stock issues that had a reserve status and that would really corrupt the IV file.  

I've also read that a Location can be deleted from Setup - Locations.  This doesn't delete the location on each item and you cannot delete a location on an item that has a quantity in the location you want to delete, even though you can delete the location from Setup - Locations.  Kind of strange. 

I think the possibility exists that an item that is a stock item could have been at one time non-stock (someone could have checked that box and later unchecked that box)  I would think this could be a cause of what you're seeing.  

Next, I would try the Report - Lists - Items by Location to see if that item exists in multiple locations.  Also, you might try the physical adjustment like the person did in the previous article.  Otherwise, you may have to call Sage and ask them to fix the file.

It does not show up and any location that is the problem we are having.  It shows as qty on hand with NO location.  I'm fairly new to Sage CRE how do you do the physical adjustment like the person did in the previous article?

Before you begin, make sure a location exists on the item's setup (even though it may have a zero count.)  IV - Help - Help Topics:  About half-way down is the Perform A Physical Count topic.  Once you click that topic, start at the top to read the steps.  However, when you do a physical, you are doing it for a specific location.  It should also update the quantity on hand.  It will also send entries to JC and General Ledger when you post your physical.  If you do this, print it every step of the way and review the printouts with your bookkeeper asap because those entries may not be valid entries for General Ledger.