Cpec will stabilize the economic sector of Pakistan, as it is a flagship project of BRI.
When a dependent clause follows an independent one, a comma is usually not needed between them.
Owl Purdue explains.
don't put a comma after the main clause when a dependent (subordinate) clause follows it (except for cases of extreme contrast)[emphasis added]
CORRECT: She was still quite upset, although she had won the Oscar. (This comma use is correct, because it is an example of extreme contrast.)[emphasis added].
Your example does not present such a contrast and hence does not need a comma.
since and as are similar in this context, and both could be used to form the subordinate clause. A difference between them is the use of commas.
Cambridge Dictionary explains.
We usually put a comma before since after the main clause [emphasis added]:
I hope they’ve decided to come as
I wanted to hear about their India trip.
They’re rather expensive, since
they’re quite hard to find.
Your example uses as and hence does not need a comma.
I sometimes use a comma for clarity if the independent clause preceding the dependent one is long. The first clause in your example is not long and hence should not need a comma after it.