Regular PrestaBay synchronization works only if you change product QTY using backend interface. 

For cases updating stock level using third-party tools (like CSV import, direct DB change) we have a particular task named "Resynchronize QTY". 

You can find this function in Synchronization option.

When job run it's performed, compare between data in PrestaShop products DB table and data know by PrestaBay. If there any difference (PrestaBay think product have 2 QTY, but, in fact, it have 7), ebay item marked as revise needed. 
After revise done in PrestaBay saved correct data of PrestaShop product QTY. 

Please notice that any QTY synchronization work for Selling Profile QTY modes "Product QTY" and "Not more that QTY." For other modes, QTY synchronization does not work.