you can call and waitlist those business class seats. If they have them available closer to flight, they will call in the order of status. In my experience, that can be anywhere between a week to 2 days before the flight. It is also quite possible to upgrade at the gate too if a business class passenger doesnt show up. but from experience, its very often overlooked. Make sure you tell the ground staff, also ask the flight attendant. this is a hit or miss though at the last minute.

but you are correct, if you transfer miles in and do not get upgraded, your miles are now stuck at eva for 3 years? i think. This is def a chance. Sometimes the reps can tell if your chance is good or not to upgrade, worth asking when you make that call. (also good luck on getting a rep on the line ^_^)