Ok. We found a problem. After recovering a gone portal , we saw that the PDM Library ID's does not tie to what has been defined on the WCM ID. Now, we have hundreds of WCM content that references hundreds of documents so updating them is really impossible. However, there's a technique to do this.
The table ICMUT01424001 of the WebSphere Portal under JCR schema contains the references of all the PDM. What we did is to update the ID (the numeric number between ). Since when importing PDM, this number is auto-generated thus losing the references from WCM. So we updated the table data to fix this.
The link : http://www-1.ibm.com/support/docview.wss?rs=203&context=SW000&dc=DB510&dc=DB520&dc=D800&dc=D900&dc=DA900&dc=DA800&dc=DB530&dc=DA600&dc=D600&dc=D700&dc=DA500&dc=D200&dc=DA410&dc=DA450&dc=DA430&dc=DA440&dc=DB540&dc=DB400&q1=database+table+usage&uid=swg21255445&loc=en_US&cs=UTF-8&lang=all contains the list of Tables WCM uses (WCM Tables). This is very helpful if you want to know more about WCM/JCR Tables of WebSphere Portal