I reduced our number of documents, which were numbered like ISO9002:1994 before I got here, but I never changed the numbering. I merged procedures into others or eliminated them completely, but, for example, our Contract Review Procedure is still TCP.03.01 and all the resulting forms are TCF.03.whatever. The ".03" is just an arbitrary number now - it doesn't relate to the standard anymore.
Now we have a specific requirement in AS9100 that we have to take into account for clearly showing the relationship between the requirements of the standard and our documented procedures. I won't go through and change all of our document numbers - besides, so many things overlap, leaving you to choose which number it most fits. Phooey. Also, we prescribe to more than just ISO and soon AS9100, we also have Part 145 Repair Station stuff to consider in the very near futur.
I figure what I'll do is create a matrix listing our documented policies and procedures, with a column for each standard/regulation and just list the clause numbers that each procedure addresses. I can "save as" my Master Document List and add appropriate columns, but I haven't thought it all the way through yet.
As an ISO registered company, before all the AS and FAA stuff, I would have never sweated the way documents are numbered.