US:
Fire Emblem Fates: Conquest CTR-BFYE 0004000000179600
Fire Emblem Fates: Birthright CTR-BFXE 0004000000179400
Fire Emblem: Fates Special Edition CTR-BFZE 0004000000179800
JP:
Fire Emblem if: Special Edition CTR-BFZJ 000400000012DE00
Fire Emblem if: Hakuya Oukoku CTR-BFXJ 000400000012DC00
Fire Emblem if: Anya Oukoku CTR-BFYJ 000400000012DD00
Use a CIA installer like FBI, BBM, or DevMenu and uninstall whatever game you have installed. You said you want to delete the Japanese game installed, so just find the serial/titleid and delete. You're most likely using the Japanese Special Edition, so look for CTR-BFZJ (serial) and/or 000400000012DE00 (titleid).