Hi all, thanks for being some of our first adopters of Fleet and Elastic Agent. It seems you all have encountered one of our rough spots in integration upgrades. This is definitely not the experience we want and is something we're planning to address in an upcoming release as part of [Fleet] Handle common transient errors during package installs with a retry · Issue #111859 · elastic/kibana · GitHub.
In the meantime, there is an API workaround you can use to force these assets to be reinstalled without having to wipe everything and start over. This command will force the base package to be reinstalled:
curl -XPOST \
--url http://<your kibana host>/api/fleet/epm/packages/system-1.1.2 \
-u <username>:<password> \
-H 'content-type: application/json' \
-H 'kbn-xsrf: x' \
--data '{"force": true}'
You'll want to be sure you use the correct version number at the end of the URL (I used 1.1.2 here). You can see which version is currently installed by visiting http://<your kibana host>/app/integrations/detail/system/settings. This can also be used for other packages as well, just change the system in the URL to another package name and use the correct version number.
I hope this helps!