I'm not sure what you're trying to do here, but it looks more complex than I'd expect.
You could just open /dev/uart232 and read from it, writing to /dev/uart1 when there is data available.
But if you want to do this from interrupts then you need to stop the HAL from attaching its drivers to the UARTS you are using.
I suggest you stop at alt_main() and step through that function and through alt_sys_init.c to see what's going on. There's a tickbox in the launch configuration to make it stop at alt_main.
To replace the HAL's drivers you should copy the appropriate files from the altera_avalon_uart directory into your
system project and edit them there. The build system will use your copies instead of the shipped ones and you can edit as much as you want.