Sorry to say, I had the exact same issue with my 2003 ar 6mt. Audi uses a stupid plastic face on the release bearing. Exact same symptoms happened to me. Refused to engage. Then a day later, worked fine. Then nothing. Pulled trany and found the plastic face on the release bearing was disintegrating, preventing engagement. Indie suggested SOLiD face release bearing, like used by racers. These don't wear out.
Did new disk and PP since the trany was out, even though they were still in great shape at 90k.
All because of $1 piece of plastic on the release bearing spec'ed by Audi.