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I agree that it would be very nice to have a correct sorting in the web as well (in my Mac the Zotero app works fine). My list (in the web) stops at call number 999, instead of continuing with 1000, 1001, etc.
I exported my Endnote library as "text only" with "RefMan (RIS) Export" style. Then I replaced every "LB -" (where I had my custom numbers in Endnote) with "CN -" (Call Number) in the output file. And finally, I imported that file into Zotero. Fo…