In Biopython, something like this should work

from Bio import SeqIO
my_record = SeqIO.read("input.gbk", "genbank")
reversed_record = my_record.reverse_complement(id="new_id", ...)
SeqIO.write(reversed_record, "output.gbk", "genbank")

The tricky part is deciding which of the annotations like name etc should be kept or replaced.

You could try Pagit from the Sanger institute. It contains a program called abacas that does contig ordering using mummer and gives you a fasta file of the ordered scaffolds and a genbank like feature table of how the contigs were ordered.