Start by downloading(Export) your store stock file from your store Admin Panel > Tools > Stock Control
Once downloaded the stock file (in Excel XLS or TXT format) you can edit the contents under "SKU" column and save file.
Now you can upload (Import) the edited stock file back to your store from Admin Panel > Tools > Stock Control
Please allow a few minutes for the database to process the updated stock file.
Upon completion of database process, your products (and variants) will have the new/updated SKU information applied.