By default, DITA2Go does not create an external version of the drop-down JavaScript code. To have DITA2Go write the JavaScript code to a file in the project directory, when you specify a file for DropJSLocation:
[DropDowns]
; WriteDropJSFile = No (default, you provide it) or Yes
WriteDropJSFile = Yes
When WriteDropJSFile=No, DITA2Go assumes that the file you specified for DropJSLocation is an existing JavaScript library that you do not want overwritten.
When WriteDropJSFile=Yes, DITA2Go overwrites the file you specified for DropJSLocation if it is in the project directory, or creates the file if it does not already exist in the project directory.
WriteDropJSFile takes effect only when DropJSLocation=filename (see §16.9.7.2 Locating JavaScript code for drop-down sections). And while any path information included in filename is used in the link in the <head> section, DITA2Go writes the file itself to the project directory, for security reasons. This means that if DropJSLocation specifies a location other than the project directory, you must move the file to the other directory.