I have the latest 4.1.27.0 version of Express running on Win10 x64, and an Edge 1000 running F/W 9.10 with several IQ apps installed. I have the Auto-update apps option "Automatically update Connect IQ apps on your device when syncing" checked in Express. However, when apps are updated on the IQ store, a) Express doesn't update the local copy of the app when syncing, and b) when I have manually updated the local copy of the app, Express doesn't automatically send the updated version of the app to my Edge 1000 when syncing.
The procedure I have to follow to get an update onto the 1000 is to a) go to apps.garmin.com and manually download the updated app to Express; b) click "Manage Apps" in Express and click the "X" in Express to remove each app that I want to update; c) click the download button in Express to send the updated app to the 1000.