(4.40) output: (prop_laser_catcher,battery-catcher) -> (battery-relay_powered,Trigger)()
(4.40) input battery-catcher: battery-relay_powered.Trigger()
(4.40) output: (logic_relay,battery-relay_powered) -> (battery-branch_powered,OnProxyRelay2)()
unhandled input: (OnProxyRelay2) -> (logic_branch,battery-branch_powered)
(4.43) input battery-relay_powered: battery-relay_powered.EnableRefire()

This comes from the console with developer 2 on. It says that the laser catcher triggers the relay called "battery-relay_powered". Then on the third line it says that that relay is going to send an input called "OnProxyRelay2" to "battery-branch_powered".

Now, "battery-branch_powered" is a logic_branch, so telling it "OnProxyRelay2" doesn't make sense to it, ergo the fourth line. What this means is that the relay has an output "OnTrigger, branch_powered, OnProxyRelay2". I should mention everything is in an instance and has the "battery" prefix as a fix-up name.

What is strange is that this relay's output is actually (when viewed in Hammer) "OnTrigger, branch_powered, Test". What's going on here?

If you decompile maps with instances, the decompiler will create OnProxyRelay1, OnProxyRelay2 and so on. They don't exist. Thats just how the decompiler handles instances.
There is just one output of the instance proxys: OnProxyRelay

I think I know what you're saying, but I don't see how it helps me. I think you misunderstood what my problem is. The i/o chain is being interrupted because of the unhandled input.

I just deleted the proxy entity from the instance and it's inputs. The instance works fine now. The i/o chain continues through with no snags. I still have a problem though. Now I can't output anything from my instance since I can't put a proxy entity in it. When I put the proxy entity back in, it stops working again with the same problem.

bump I still haven't figured it out.