BRUSSELS—U.S. sportswear maker Nike on Wednesday lost its fight to stop a probe into its Dutch tax affairs, as Europe’s second-highest court backed an EU investigation opened two years ago. The EU case was part of a crackdown on multinationals’ sweetheart tax deals with EU countries that Brussels says gives them an unfair advantage, among them Apple’s Irish tax arrangements, and Fiat Chrysler, and Amazon’s Luxembourg deals. The Luxembourg-based General Court dismissed Nike’s challenge against the EU investigation. “The [European] Commission complied with the procedural rules, and neither failed to fulfill its obligation to state reasons nor made manifest errors of assessment,” the court said. Judges said the EU executive carried out its provisional assessment of the measures at issue in a diligent and impartial manner and that it did not breach the principle of good administration. The U.S. sportswear maker had objected to the Commission’s 2019 decision to investigate …