You are never going to get a concencus on this one because it is up to each Member State to decide how it will deal with its own licence when a JAA licence is issued. For once, the JAA is absolutely unequivocal on the matter, JAR-FCL 1.065 (d) reads:
An applicant shall hold only one JAR-FCL licence (aeroplane) at any time.
Notice that this refers only to JAR-FCL licences, it doesn't bar you from holding a national licence in addition to a JAR-FCL licence.
The UK CAA have interpreted this as meaning that they do not have to cancel a UK licence when they issue a JAR-FCL one and so pilots obtaining a JAR-FCL CPL, on the basis of a national CPL, in the UK will retain their pre-existing national CPL. Provided that this licence is maintained in accordance with national rules, any attendant ATPL theory credit will remain valid and it will be possible to add a multi-crew type rating to that licence and, on achieving the required experience, to obtain a JAR-FCL CPL(A) with ATPL theory credit in accordance with Appendix 1 to JAR-FCL 1.005 (Case 4).
The above, however, applies only in the UK. Other JAA member states have decided that they will not allow their national licence to be held alongside a JAR-FCL licence and, in the event that a JAR-FCL CPL is obtained on the strength of a national CPL, any attendant ATPL theory credit will be lost. If you hold a non-UK national CPL, you will need to check the rules with the state concerned.
It is always possible, of course, that the JAA will tumble to the UK's liberal interpretation and act to close this particular loophole and so I would not guarantee that the situation will remain the same after July 2002.