First point is that GST is not coming into effect from 1st April 2010... so u have time for adjustments...
The white paper released on GST is silent on the credit of various duties already taken or to be adjusted under previous laws... So any sure shot treatment cannot be given...
The Query u have asked is a perfect example of the legal risk associated with a business. the law is changing and it may turn out either way... So in my personal opinion u should avoid carrying forward of any Credit to the GST era.. because it may happen that credit of some duties may not be allowed to be adjusted or carried forward. ... try to utilise it fully before GST itself.. This opinion of mine is very personal in nature so if u think otherwise than u can do so... This view was originally given by CA Ajay Jain, renowned teacher of Indirect Taxes, but they also said that this is their personal view.