I'm afraid you may not have told us enough information about your problem for us to help you.
You can create lines in InDesign with the Line tool or the Pen tool. In the current version of InDesign CC 2014.2, both should be retained when exporting to EPUB.
You may find discrepancy while exporting some compound paths to epub.
Hence it is required to rasterise the same using Object-->Object export options-> Epub & HTML--> Preserve appearance from layout-->rasterise container/Content.
This should help you. Your content may be turned into image but the appearance is retained.