I know Bigasoft FLAC Converter is professional audio converter for FLAC conversion. It can batch convert thousands of FLAC files to Apple Lossless directly, as well as convert FLAC to MP3, WAV, AIFF, and more audio formats.
Here is a step by step guide for converting Apple Lossless with Bigasoft FLAC Converter
http://www.bigasoft.com/articles/how-to-convert-flac-to-apple-lossless-audio.html