Sorry for insisting on this, but grammar terms confuse me; usually,
I'm better able to understand things through examples.

So, lets take the initial Ca'NoN sentence..

{qarDaSQa'Daq ruDelya' rop'a' Hergh qengbogh yo' Dabot}
Intercept rudellian plague relief convoy to cardassian union

Suppose we altered/butchered it, by writing:

{qarDaSQa'Daq Dubot ruDelya' rop'a' Hergh qengbogh yo'}

In the altered sentence, could the {qarDaSQa'Daq} still refer to the
{ruDelya' rop'a' Hergh qengbogh yo'} ? That is, could it mean "the
rudellian plague relief convoy to the cardassian union intercepts you"
? Or the only way this could be interpreted is, "the rudellian plague
relief convoy intercepts you at the cardassian union" ?

It could only be interpreted as the latter. You've "split" the -Daq noun from its clause and stuck it on another clause.

This is the intended relative clause: qarDaqQa'Daq ruDelya' rop'a' Hergh qengbogh yo' fleet which carries Rudellian plague medicine to the Cardassian Union.

That clause is a single noun phrase. Think of it as a unit. X = qarDaqQa'Daq ruDelya' rop'a' Hergh qengbogh yo'.

The main clause is X Dabot.

Just put the relative clause X in its place.

If you wanted to say the fleet carrying Rudellian plague medicine to the Cardassian Union blocks you, it would be Dubot X. You have to put all of X where the X appears. You can't split pieces of it to go somewhere else in the sentence. Dubot qarDaqQa'Daq ruDelya' rop'a' Hergh qengbogh yo'.

-- 
SuStel
http://trimboli.name