OK IM PISSED AND IM DONE!!!! Iv never EVER come across a game THAT FALLS APART AS U PLAY... Im tired of things working then all the sudden stops working.. Im fucking done..... I started a new game to see if I can unlock the damn trading Start THAT MAGICALLY DISSAPPEARED OFF THE DAMN START MENU.. And now BOSA TA (the guy that blows up the Tear in space) Well the bastard is blowing up MY FREAKING SHIP!!!!! Not the 1 im putting in range BUT ME... YES I DONT HAVE THE ANTI_MATTER CELLS... IN MY SHIP ITS IN THE SHIP I WANT HIM TO BLOW UP BUUUUTTT NNNOOOOOOOOOOOO JUST BLOWS ME UP over n over again no matter what I do or how I fucking do it..... Im done, I realize I sound like the others but idc anymore.. only thing I can think of to "WORKAROUND" it (which is another thing im sick of doing, shoudlnt need to "WORKAROUND" anything!) is docking both ships and Swapping everything, which is a stupid waste of time when it should be working correctly in the first place, I almost quit because my trader start disappeared and I was trying to get it back but now I cant even complete this mission.. SO I quit..
(Im sorry about my anger)

You should do it from the start with your starter ship so you don't have to fire anyone.
Put antimatter in store, leg it to the 1st point; the space walk to the second.
I actually managed to somehow keep both ships in my run; one inside the magical asteroid that i no-clipped to while space walking.
Anyway... then you purchase a new ship from I guess argon wharf, when built (from the map screen) click on it's icon and right click next to yourself and direct order it to go there.
When it arrives spacewalk your ass within 400meters and commence docking.
With only one ship to blow up it can only blow up one ship; and since it's a scripted event once that scripts run no more blowing up.
If you get harrassed by the galaxy shake an bake 'I materialize from nothing' xenon raiders, just space walk into the struts of the newly generated space turd base and get your ride to come in close via more orders.

Personally i'm currently hating the black market runs.
Dodgy guy in a bar gives me quest; hang onto some illicit goods till you have enough then get them to me.... Then he goes and hides INSIDE a base.
Yep no bar to meet him at; as soon as ya dock there goes autoguide orange on the fritz no way to find him.
Just keep on holding those goods that if your scanned just before docking will have the whole station firing at you...
Freakin space trolls.

Looks like the game wants to kill the starter ship. I always let it blow up that ship, never tried any other way.

I guess the Devs never thought people might try alternative ways, or they never had time to cater for that. And you`re right, the logic should be that the ship with the anti-matter should blow.

I understand your frustration, this game needs at least 6 months more of work imho.

I blew up a second ship, though I did have to redo the quest because the first time the "You're clear, I'm gonna blow it up" event triggered before I was clear...

The strange thing is Iv never had this issue before until after Their "Hq Bug fix" idk what was broken before but now deff broken lol Also can tell its bugged as he isn't giving me the waypoint to get clear like he normally does, iv done this mission a few times and this is the only time iv come acrossed this issue.. ya they deff released to early just ot get Xmas sales :/

Might not be a bad idea to play something else until v2.0.1 comes out.