I'm in chapter 3 and decided to go with Bodhi, and for one quest wanted to go back and fetch Yoshimo from the CopperCoronet, but he done flew the coop! Will he come back to me? I hope so, as he has a few items I'd like back...

Nope he's gone forever ;] I think you'll be able to get back your things later (You should meet him later..just continue your game)

Go back to wherever you left him and he'll probably be standing there. We've found that characters (Yoshi, Jan, Nalia, Valygar...) who get kicked out of our party just stay where they are, no matter what we tell them to do.

I am quite sure that if you do not have Yoshimo in your party when you start chapter 3 and side with Bodhi, he leaves for good.

I did not accept him in my party in the dungeon, so he went to the coronet. He was there until I sided with Bodhi - I go back to coronet and he is gone for good.

Don't you need Yoshimo? After all he can defuse traps, so take the job of Imoen? Who'll you take from Copper Coronet? Aerie from the Circus? Nalia, Anomen from the Coronet? Perhaps Korgan? I'm planning playing it with a fighter, so maybe I'll take Anomen and Nalia...