How to handle possible cross link penalty

[chaneguye]

We have two site that we run on the same server. Several months ago we added some cross links between the sites as they are relevant and we wanted to drive cutomers to the newer site. Since that time our Google referrals are way down and about half of our pages have been removed from the index. Furthermore, about 90% of the pages that are currently indexed show only the URL with no title or description.

We have just added nofollow tags to all of the cross links. Is there anything else we can do to help reverse the problem? How long should we expect it to take before things start to turn around?

Thanks