Since 1994 version, one of my ISO9000 system design rules for small businesses is to maintain a document numbering system only for drawing numbers.
The results have been no wasteful cost to maintain document number systems and above all, when the companies are doing transition to 2000 version, the systems makes transition cost very small, because almost of companies which have document number systems have the clause numbers of ISO9001: 1994 (from 4.1 to 4.20) within the document number digits and with the change of the clause numbers of ISO9001: 2000, all document numbers have to be changed. The changes will make transition cost high.

I am used to propose to companies that have such problems, stopping documentation numbering system at the transition. For all present documents with numbers you should paste white tapes on them and new clause numbers will be pasted only backbones of files or tags for easy retrieval by new clause numbers.

There is another alternative to leave as they are, but old different clause numbers will make meaningless confusions.