Can I modify the quantity in stock for a part, whose shelf life has expired?


Yes. You can do it following the following route: Inventory>> Manage Inventory>> Warehouse. 
 
Once you enter the Part number into the dialog box, all the stock-related information on the part will be retrieved. 
 
Click edit and make the required changes.

 
Bonus tip: There might be some cases where you will need to make changes to multiple items that either share a part number root or are different instances of the same part (with different serial numbers). To retrieve the complete list, you may filter by the common number digits or description name plus an asterisk.