Original sentence.
a) The reason being that you will be free from extra shipping for the transfer.
Can we reconstruct the sentence as,
b) This is being to make you free from extra shipping for the transfer.
Original sentence.
a) The reason being that you will be free from extra shipping for the transfer.
Can we reconstruct the sentence as,
b) This is being to make you free from extra shipping for the transfer.
Your suggested re-write of the sentence, unfortunately, is not grammatical.
Maybe part of the problem in your understanding of the original is that your quotation does not seem complete.
When we say "the reason being that..." it normally follows a statement and is linking that statement it to the reason why, for example:
I went to bed early, the reason being that I was tired from the previous day.
Your sentence contains a reason but does not say what it is a reason for.
You could rewrite my example as:
The reason I went to be early was that I was tired from the previous day.
or simply:
I went to bed early because I was tired from the previous day.
my question is about using "This is being to" is correct or not
Well, in your example b), it is not really correct. I would say it like:
b) This is done to make you free from extra shipping for the transfer.
However, Mari-LouA's comment makes a lot of sense (as in: it fits the context and the specific terminology much better):
This is to exempt (free) you from extra shipping charges...