Hi,
Well, you finding the issue with the "restrictions and dimensions" settings only confirms the diagnosis I made.
When the server is restricting the number of parameters that can be received, all the parameters above that limit will be ignored.
So that means that all the options displayed after the "breaking point" in the interface will be ignored by the server.
You've increased the max_input_vars variable of PHP but did you check suhosin's configuration ? You can find more information on that in the second answer of the link I gave:
stackoverflow.com/questions/9399315/how-...post-variable-in-php
Suhosin's settings is a common cause for that problem.
If that doesn't work either, I could have a look at your backend, but so far, in the last ten years of supporting HikaShop, each and every time this issue was reported to us, it was because of a server limitation on the parameters count, nothing we could do about even with a backend or a FTP access :/