I have a TJ AWD Magna which I intend to replace the ECU. Will there be an issue with the Keys.?

I'm pretty sure the ECU, BEM (body electronics module) & key are matched/coded by Mitsubishi dealers with their MUT machine. If you change the ECU & car doesn't start you'll need to book it in with someone who can either code it to the BEM (using a MUT) or read the ECU settings & turn off the immobiliser function. If you look up Madmagna in the Mitsfix section of the forum & give him a call he'll be able to help out.

Cheers

I have a TJ AWD Magna which I intend to replace the ECU. Will there be an issue with the Keys.?

If the current ECU is still operable, then the ECU can be read and the immobiliser code copied into the replacement ECU provided you have access to an OpenPort cable (1.3U or 2.0) - more info in sig link.