If the files you are converting have no interfile links, you do not need.ref files. However, if there are interfile links, .ref files are essential to make any links to split parts point to the right split file (see §17.2 ).
By default, Mif2Go deletes *.ref when EmptyOutputDir is in play (see §33.3.1 ) and there is no explicit setting for EmptyOutputFiles (see §33.3.2 ). When reference files are removed, you lose the information added from other books or files that were already converted. If you are running a series of such conversions, you can delete *.ref files before the first conversion, but not thereafter.
On the other hand, a .ref file might actually be inaccurate if it covers a version of a file that has different page breaks; and .ref files clutter the project folder. It is best to remove them when you are about to reconvert an entire book.
When you are converting a single file with external links (such as a chapter of a book), for links from the file being converted, the .refs for the files referenced are needed. For links to a file being converted, the .ref for that file is needed by the other files. The other .htm files are needed too, because the file being converted might patch other .htm files when references shift to a different split part. Therefore, removing .htm files is hazardous when there are interfile references of any sort; broken links can result.