Iām having the same problem in the latest ACF PRO (5.6.10).
This is very strange. On dev and local server all is OK, but on staging is problem. Supposedly another developer have been problem on local.
I found resolve for this problem š I change value for max_input_vars in php.ini for 10000 and all is OK.
I think that should be notice before save about this problem because peopl can lost their changes