We can't speak specifically to plea negotiation. We know whether or not there was a guilty plea, and in those cases the guilty plea is less frequent than we see within the data set as a whole. We expect to see somewhere around 90% guilty pleas.
The way the data are organized, if there is a conviction in the case, that offence becomes the most serious offence. So if the case is described as stayed or withdrawn, or as “other disposition”, then all of the charges in the case would have a decision that didn't carry a conviction.