The source files can be stored in a single folder or in multiple folders on your network or computer. When you plan to import source files stored in different folders you can use the batch import option. Alternatively, you can complete a separate import job for each folder. To overwrite objects ensure you are importing into the same folder in your Author-it library as the previous imports.
If your HTML source files have topic-to-topic links ensure there is sufficient information in the anchor link for it to find the target file in another folder. For more information on the HTML source file location refer to Importing Files with Topic to Topic Links.