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What is the best way to create invoices with more than 20k lines.
I m trying to do append lines by multiple updates but its very very slow.
I may also anticipate future updates to this invoices what is the best way to proceed in this case?

Maybe try to make multiple invoices but use invoice grouping instead?  Once you get more than 500 to 1000 lines managing the invoice in the UI is incredibly slow and difficult
Note there is a 100 invoice limit in an invoice group 

Alternately maybe consider a custom child record that holds the detail of all 20,000 lines and do a few consolidated items/lines on the invoice
Then use a saved search template or export to show the detail of the custom record

FYI I think the limit on invoices and non-JE transactions is 5k lines if I remember correctly, so I'm not sure it will let you do that anyway. how are you trying to create these? via the API or CSV?