TwilightMenu is applying AP patches based on the game code (IREO or IREK for B2W2) and the game header CRC16 (offset 0x15E in the ROM).
The Route 10 patch modifies the header and the CRC16, so TwilightMenu is unable to find and apply the correct AP patch. You would need to AP-patch the game manually after applying the Route 10 patch.
I got it! It worked out! I unlocked my 3DS (the same one I played the game on before it corrupted), and then used SaveFL to delete the game's SecureValue, then it started working again. Thank you very much!