Your question is not entirely clear, but here is some information.
- When you are in the Timer interrupt, unless you did a cli, the processor interrupts are off, so the SCI interrupt would not happen until you reuturn from the timer interrupt.
- There is no reason why the 2ms interrupt should be lost, unless there is a bug in the code, like not clearing the SCI interrupt in the interrupt handler, but the the whole program should crash.