The idea of the players never finding out what was so special about the X-boat, but still being able to prove the 'bad guy' guilty of wrong-doing is not a bad one.
That's somewhat my thinking. Rather than a message which has been missing for 27 years finally come to light, it's an object which was reported 27 years ago to be aboard the X-boat not found aboard the X-boat. The questions then begin.
Who said the object was aboard? Why did they say that? Where is the object now? All those questions, and any others, are going to stir up a lot of trouble in certain quarters.
I guess I looked away from the missing message angle because any important messages are going to be backed up. The senders will keep a copy or the message will be sent twice or something else. The Armbruster Will? The lawyers will have another copy. Orders to the 117th Provisional Mobile Laundry Service? They're filed in triplicate. Bucky's thank-you note to Aunt Sally for his birthday gift? It's on his tablet. Nothing along those lines are going to be lost "forever" when some X-boat misjumps.
A one-of-kind physical object or a group of objects however? Now we're looking at something that can be lost. The Teasdale Cocktail Umbrella Collection? Gone forever. Achenbach's
Shemp by Moonlight? Never seen again. Slappy Critser's 800th homerun ball? It's out of here.
So, the players board X-boat Alpha-Jay-Niner-Three-Stroke-Umptyfratz, do a quick survey, pack up the body of the unlucky pilot, nudge her into a long orbit around the local primary, return to the starport for their reward, and almost the first question they're asked is
"Was the Achenbach painting aboard?"
The players answer that they don't know. They did a fast check, made sure the non-volatile message bank memory was still intact, and grabbed the pilot for burial. They didn't break into the 1dTon cargo locker because, among other things, they're not thieves.
By this time a local patrol cruiser has docked with the 'boat, strung a power umbilical, and it slowly powering up the old 'boat's systems. The cruiser's crew break open the cargo locker because they're the authorities and - surprise -
Shemp by Moonlight isn't there.
That is when the real questions start to be asked and the
real adventure starts.