If playing on a PC emulator like Yuzu or Ryujinx , you must use the "Install files to NAND" option. After selecting the update NSP, verify the version number in the game's properties to ensure it has been applied correctly.
If you followed the steps above and Digimon World: Next Order still refuses to load with the update, use these targeted troubleshooting techniques. The Game Asks for a System Update
Nanomon pointed to a towering spire of jagged, red-hot data. At its base, a was gnawing on a string of code labeled 'Loading_Times_Optimization.'
Source: Perfectly Nintendo & Official Twitter announcements
Before transferring any files, ensure your base game and your update file belong to the exact same game version and region (e.g., both are the US/NA region).