Does it change SKUs?
No. SKU Stock Sync does not change your SKUs.
The app uses existing SKUs in Shopify to decide which variants should be grouped together, but it does not create, edit, format, or rename SKUs.
If you change SKUs in Shopify, SKU Stock Sync may need to detect and prepare the updated grouping before those variants can sync correctly.
If two variants should not share inventory, make sure they do not use the same SKU at the same Shopify location.