Hi,
Thank you very much, this helped me a lot. This took me a while to figure out, but I managed to solve it. Turns out a certain PHP core function (parse_str) is also limited by the input variable limit. This is an issue, as it is not even documented in the PHP documentation.
I had to search for an alternative parse_str implementation, luckily other people had this issue before, and there was a solution. I have implemented an additional code section to resolve this.
I will of course inlcude this in the upcoming release. Hopefully everything should be saved correctly now.
I still highly recommend increasing the max_input_vars limit to above 1000, as other plugins may use more than 500 variables easily, and it is not easy to bypass that limit otherwise.