1. You should check Items with wrong balance, if they are used with serial number tracking or none, for that use Item History report and see the documents in which they are, then look at Serial number column

Item card

Item Histrory

 

Goods receipt

2. When the Item card is checked then you should depreciate all the balance of that Item.

To see what quantities you have and in which stock use Stock list report with Radio button 'Per location' 

 

For depreciaton use Depreciation. Better use one depreciation for one stock so if you have item in two stock then two depreciations.

 

 

Also if Item is with Serial number, then you should Depreciate all balances for Serial numbers

 

 

3. When the Item is depreciated then chek reports Stock list and Item history for that item
4. If everything is ok make Goods receipt , with right quantities and cost price. Also if you should receive in two stocks then make two Goods receipt documents.