You can edit your save. There is no other way to change your Ship Prefix in an ongoing game for some insufferable reason probably related to the equally ridiculously absurd reason why you can't change or even decide on Monarch/Heir names.
Search through the save for your Empire Name, or for the "country={" entry because the Player Empire should be first. Then search for "ship_prefix" and the one it takes you to should be your Prefix. Modify it to what you want, then recompress your save game files (both of them) into a .sav archive with 7zip while specifying the parameter 'tc=off'.