I see that my last few runs no longer show data in the cadence chart. The cadence data is there and can be seen on the splits screen, but the chart for cadence is empty.
No, no, no. You are spreading so much misinformation.
First, the data files have always been stored locally (except for a brief time with Garmin Express). The ANT Agent stored them on your PC, and recent versions of Garmin Express store them on your PC. When you upload your data to Garmin Connect, you are uploading a copy of this data to Garmin Connect, so they have a copy of that data.
Second, you don't have to use Garmin Express to upload your data to get cadence to appear. The mechanism you use to get your data to Garmin Connect does not matter. Your cadence graph will disappear if you set your activity type to anything other than Running or Cycling. This is a known issue, and it affects all Garmin Connect users. Changing the activity type is the cause of the problem.
Third, Garmin hasn't lost the cadence data for your old activities. It just isn't visible if you are using an activity type that exposes this bug.