For script operations, Subdirectory search/replace is enabled /disabled as follows:
If ‘Use Program Options’ is selected in the Scripts-Advanced tab, the script follows the subdirectory setting currently in effect for the program. The ‘Search Subdirectories’ field on the Scripts-Advanced tab is dim and not available.
If you specify different Options for your script, the ‘Use Program Options’ checkbox in Scripts-Advanced will be unchecked and ‘Search Subdirectories’ is now available to be changed.
Subdirectory searching will usually slow your search so turn it off if you only need to search the specified path.
Note: As of v 4.6 you can limit how deeply the program will recurse within subdirectories. See the Special Registry Switches topic and scroll to the ‘ Limit Subdir Recurse Levels’ section. Alternatively the switch can be set using the special configuration utility on our www site. Visit the Search and Replace page to download the utility.