I had the same issue and found this article helpful:
https://webcusp.com/solved-how-to-increase-wordpress-menu-items-limit/
Adding the .user.ini file to my root folder did the trick for me. Here are the instructions:
Create a file .user.ini and add the following code to it and try placing it in WordPress root or in wp-admin folder;
max_input_vars = 5000;
I created the file in text editor. I had to add the first period to the file after I uploaded to the ftp site, so it wouldn’t “hide” the file.
Good luck!