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Recope filed the suit in April 2014 after the comptroller invalidated a project study amid alleged irregularities.
In a statement, the company said it withdrew the claim after the board of Soresco, established with CNPCI to undertake the overhaul, did not reach an agreement to carry out a new feasibility study as called for by the comptroller.
The board also failed to reach consensus over a reduction of operational costs at the JV, which has received US$50mn each from Recope and CNPCI.
Recope said Soresco will hold an extraordinary meeting to identify project alternatives.
According to preliminary information, the US$1.5bn modernization project aims to increase capacity to 65,000b/d from 25,000b/d, and produce cleaner products.