A client turns up with a pile of paperwork long before there are any proceedings. That paperwork now lives in the matter, the client's folder where you gather it and classify it; on top of it you then build the case file for each set of proceedings, with the pieces that belong to it. The same document serves two case files without you duplicating a single file, and in each one it carries its own annex number, the one you will cite in a pleading, in the format you choose.
The paperwork starts in the matter
New documents go into the client's matter first. JUDLEX puts forward where each one belongs and you confirm it; anything it cannot identify stays visible as unclassified instead of being filed on an assumption.
One document can sit in two case files
You build a case file over documents that are already in the matter, so the same piece can sit in several. In each one it carries its own annex code, its order and its folios, the page numbers you cite it by, and there is still one file on disk.
You choose the numbering
Each case file has a type — civil, criminal, tax — and that type puts forward a numbering family and a display format. Changing that choice alters how you see and export the annexes, not which document is which.