Any plugin that has activity data or writes data to WordPress tables in the live environment, and that data or transaction only happens on the live site (ie Security plugins) will have its data immediately overwritten and lost any time a Staging publish for unrelated content update/publish is performed.

This issue almost nullifies using the Staging environment as there will be many instances where there is data that is different in live, that would not be present in Staging environment, especially since there does not appear to be any sync functionality.

If there is no way to make publishing a merge, update, or additive function, then we should have the option to select which tables get published (ie.. post, page level content only) vs just a complete database overwrite.