I find this confusing, as the intelligence window reports the correct long name, race portrait, and flag. So, why would the handle be different from the short name? Unless, in your mind, the short name is not the handle but something to use somewhere else. But then, where?
The Race Short Name is used for places where the Race Title would be too long, such as colonies on the System View.
The three letter capaitalised abbreviation on the intelligence window is a reporting code and is used for contacts. This is initially set to the first three letters of the intelligence reporting name. This reporting name is always the <system name> aliens until comms are established, after which it will change to match the long name. Also, you can change the reporting name and the abbreviation to anything, regardless of the alien's actual name. So if you discover the aliens in Wolf 359, they will be named the Wolf 359 aliens and their reporting code will be WOL. In your case, I am guessing the two races started on the same planet so comms were already established.
So the reporting name and the three letter abbreviation are completely independent of the true name of the aliens, with the only crossover being the reporting name updated once comms are established.
For example, in my own current game, my race short name is Imperium, which would be too long for contact information.