Hi xanthonius,
Might be too late, but I just had a similar issue and found this thread. For me it was caused by max_input_vars being set too low in php.ini.
This setting controls how many variables will be accepted by PHP at once. Building a large ACF field group in the admin can require sending hundreds or thousands of variables to the server on save, so if max_input_vars is set too low and the field group you’re building is too big, your data gets truncated when you save it – in this case, probably in the middle of a conditional logic section.
PHP documentation for the setting is at http://php.net/manual/en/info.configuration.php#ini.max-input-vars, but if you google ACF max_input_vars you’ll likely find more relevant help.
