File Operation Options
Tools > Options > File Operations
By default, Beyond Compare prompts for confirmation before performing various actions. Unmark any of these checkboxes to suppress the confirmation dialogs.
Pick Prompt, Yes to All or No to All to control confirmations that might appear during a Folder Compare session's synchronize command.
How filters affect file actions
By default, file filters and display filters are respected during file actions (such as Copy, Move and Delete), unless Suppress Filters is on. To change the default behavior, mark the Include hidden items by default checkbox.