It's probably safe to say any long term player lost every Pokémon they raised and trained in any of these games; Red, Blue, Yellow, Gold, Silver, and Crystal.
I happen to have lost a Suicune in one I think Gold. What makes this so sad is I was training with only one Great Ball and on random chance ran into Suicune. I had no way to stop it from running and knew it would run after my first turn. I took the chance and threw the Great Ball and despite it not being damaged or inflicted with a status I caught it. Immeadiatley made it part of my team.
I remember my first team in Red though that was trained up so hard, all the way to level 100 without the rare candy glitch to get the job done. I moved them over to Silver, my prime game. They're also gone.
Can't say I really lost any friends though, and that might be a good thing.