Nasty problem, i suggest to first decide teh master side for one time on ;)
then use serch command and check for mirror feature. Name and study each of them and then replace mirror with just rotation to the right side. It's a pain job but that's the way to get out.
Other solution faster but...
As far as I know, in CATIA composites haven't any automatic joggle features (like aerospace sheet metal joogle command). So you need to buid the joogle manually or by a custom made powerfeature. This is an interesting functionality i was asked by a client few weeks ago, but I have still to...
