Confirmations:
By default, Beyond Compare prompts for confirmation before performing various actions. Unmark any of these checkboxes to suppress the confirmation dialogs.
The Beep after long file operations option causes an audible sound when file operations such as copy and move are complete, unless they take less than 3 seconds.
Synchronize confirmations:
Select 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.