I thought it would be safer to copy it in the functions.

Yes it would be safer.

So, what your saying is if I returned @bonly (as below), perl will not copy it will just give me pointer:
@bonly = deDuppedArray(\@currentListing, \@previousListing, \@isec_plus_bonly );

No, the list returned from deDuppedArray() will have to be copied to assign it to the array @bonly.

My original problem is @bonly changes after the function call and before function ended? Do you know why?

From the code you posted, there is nothing in the deDuppedArray subroutine that modifies @bonly, directly or indirectly, so no, I don't know why.    What sort of changes are you seeing?