Many users get confused and think that "reprice" in skugrid means to change only price. In skugrid, reprice means to change price and/or stock. In order to change only stock, your items must not be paused and must have the marketplace set (ebay us, ebay uk, amazon us, or amazon uk) and the reprice sku (item id/asin) must also be filled in. Set Pause Repricing to No.
In your settings for eBay, go to Settings --> Marketplaces --> eBay --> US or UK
Set Auto Update eBay Stock to Yes and Auto Update eBay Price to No.
If you are selling on Amazon, then to access the settings, go to Settings --> Marketplaces --> Amazon --> US or UK. Set Auto Update Amazon Stock to Yes and Auto Update Amazon Price to No.
With this setup, skugrid will only change your stock and not your price for all items in your account.