If the product is on sale and you change the price manually in the Products section of the Store admin, then the app tracks it as a price conflict. The product will be added to the Price conflicts section and the appropriate notification will be shown in the Sales log section: "Skipped. Product is in unresolved conflict.".
The app can't decide what to do on its own. You can decide it though.
The app offers the following options possible:
1) Set as regular price. This option will keep the price set by the app but when the sale has ended the edited price will be set as the regular price.
2) Set as a discounted price. The app will use this edited price as the current sale price.
3) Exclude from sale. The product will be removed from the active sale and the edited price will be set as the current product price.