Mif2Go automatically saves your document before importing a template. If Mif2Go encounters a problem during template import, and you choose to stop the conversion and investigate, do not assume that the import did not happen; some part of the import always has already taken place. Therefore, do not fix up and save the problem file; instead, just look at the file to determine the cause of the problem, then close the file without saving it. After that you can open the original file, fix the problem, and rerun Mif2Go.
When you specify [FDK]GenerateBook=Yes, the same applies to all files in the book that precede the problem file. It is not safe to just rerun Mif2Go, because all those modified files would be re-saved over your originals! Close them all, without saving.
If you are importing a template into a book, it is a good idea to exit FrameMaker, without saving files, immediately after Mif2Go finishes. That way your standard procedure can be to close all files without saving, regardless of whether Mif2Go completes the conversion successfully or stops in the middle upon encountering a problem.