Thank you for reaching out to WPML support. While you await assistance from one of my colleagues, I'll guide you through some initial debugging steps to swiftly address the issue.
1) Begin by creating a new menu on your primary language and check if it displays your other hidden menus while WPML is active.
2) It's essential to fully back up your website first. Then, navigate to WPML > Support > Troubleshooting Link and run the provided options. Be sure to avoid selecting the "Reset languages" option.