Fix the 9.90 version error
Older GEN Custom Firmware like the 5.50 GEN-D3 had a protection to avoid updating to Official Firmware and lose Custom Firmare. This protection is giving you the "system version is 9.90, no need to update".
To fix this error, follow one of the two guides below:
Fix the 9.90 version error with Version.txt Switch & Repair
Fix the 9.90 version error with Version.txt Switch & Repair Guide
Fix the 9.90 version error with DC-ARk and Ark new cIPL
Old Custom Firmware Update Guide (with Ark new cIPL and DC-ARK)