If you're stating that you have two different Lync environments, in two separate domains / forests, then you have a couple options that immediately come to mind.
Assuming you are retaining the separate AD environments. You can create a federated relationship between the two. This will naturally require the nessecary roles to be in place for external access (Edge and Reverse Proxy) in each Lync environment.
Alternately you will need to investigate Lync operation in a multi-forest environment with an identity management solution as per
http://technet.microsoft.com/en-us/library/gg398173.aspx
Naturally if there's a view to merge the two organisations into a single domain the this negates the above.
Please say if I've interpreted this incorrectly.
Kind regards
Ben