Developer Team Ninja, after announcing the Ninja Gaiden: Master Collection in a February 2021 Nintendo Direct presentation, has clarified why two particular entries in the franchise couldn’t be remastered. It all boils down to the inability to “salvage the varying assortment of data” the studio left behind.
When asked in a GameSpot interview whether Team Ninja had considered updating Ninja Gaiden 2 and Ninja Gaiden Black, producer Fumihiko Yasuda said the studio couldn’t recover both games’ data. Sigma and Sigma 2 were chosen for the Master Collection because Team Ninja had collected and organized their source codes.
“We did consider it, but we were unable to salvage the varying assortment of data we had left from Ninja Gaiden Black and Ninja Gaiden 2,” Yasuda said. “However, when we worked on Sigma and Sigma 2, we went and collected as much of that data as possible and organized it. And since we could fully utilize this data, Sigma and Sigma 2 became clear choices for [the Master Collection].”
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Source: Game Spot Mashup