I still can not understand your voip deployment in your company.
Do you deploy two voip system in your company, one is PBX and another is lync enterprise voice?
Do you mean the lync client can not call your ISDN-PBX extension? If yes, you can try to disable the CFB on the PBX.
What's the mean of the UPDATE?
You can try to use Lync logging tools to get more error logs about this problem.
Please remember to click “Mark as Answer” on the post that helps you, and to click “Unmark as Answer” if a marked post does not actually answer your question. This can be beneficial to other community members reading the thread.