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The issue is connected to the fact that current prefix for the document was filled (due to the system architecture - 1 prefix may contain 999 documents).
For solving this issue you should change a prefix for the document ( in our example it is a Customer Order) , and system would start counting document numbers again.
Go to Administration > Service Settings > Document Prefixes:
You need to change Prefix for your document type (in our case it is a Customer Order):
Open Document prefixes link - system will show the window with Document Prefixes informational register.
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