Is there a way to not receive outside transmissions to prevent the system response from being clobbered?

I am not sure I understand your question. Can you be more specific?

What product are you working with?

Are you working with Encryption?

If supported, have you set a PAN ID or Hopping channel?

To mvut:

I am working with a XBee Pro S1.

I am not working with encryption.
I have not taken into account different PAN IDs yet.
That will be dealt with later on.
Let us assume that they are all assigned to the same PAN.

The XBee is on a custom board.
The address is determined by jumpers set on the board.
These boards communicate with a Single Board Computer (SBC) for status and sensor updates.

When the board boots, I want use my AT commands to set MY address to what my jumpers say on my board.

The problem is, if the XBee was set to another address previously, it may be receiving transmissions from the SBC before it can change its address.
The problem arises when a critical board fails, the user can swap boards with a less critical board. Then the jumpers are swapped so it functions like the critical board. Now the XBee has the old address and needs to be changed to the new address.

When the board sends “+++”
I am expecting the response “OK\r\0”
But since the SBC may be sending to this XBee (wrong or right address)
I may get this “~OKI” or “OKos” or “9OsK” in my receive buffer.

I hope this clarifies the problem.

I added more details to the question. Check the comment under my question. Thank you.

The only thing I can think of that will help in this situation is for you to hold the DI line low on power up forcing command mode.