Uninstalling or reinstalling the Elastic Agent is not possible when it has been started with an invalid configuration.

[VihasMakwana]

When we try installing agent with following inputs config:

inputs:
  - type: system/metrics
    id: unique-system-metrics-input
    data_stream.namespace: default
    use_output: default
    streams:
      - metricsets:
        - cpu
        data_stream.dataset: system.cpu
      - metricsets:
        - memory
        data_stream.dataset: system.memory

  - type: system/metrics
    id: unique-system-metrics-input
    data_stream.namespace: default
    use_output: default
    streams:
      - metricsets:
        - network
        data_stream.dataset: system.network
      - metricsets:
        - filesystem
        data_stream.dataset: system.filesystem

the agent installs successfully but fails to run with

Invalid component model: failed to render components: invalid 'inputs.1.id', has a duplicate id "unique-system-metrics-input". Please add a unique value for the 'id' key to each input in the agent policy

becasue both the inputs have same id.

However, when we try to reinstall agent with correct configuration , it fails with following logs:

# command

sudo ./elastic-agent install --develop --unprivileged --force 

# output

Unprivileged installation mode enabled; this feature is currently in beta.
Installing into development namespace; this is an experimental and currently unsupported feature.

[    ] Uninstalling current Elastic Agent - Development  [0s] 
[    ] Stopping service  [0s] 
                              

[    ] Successfully stopped service  [0s] 
                                          

[   =] Stopping upgrade watcher; none found  [0s] 
                                                  

[   =] Failed to uninstall agent  [0s] Error uninstalling. Printing logs
2025-06-25T12:07:34.937Z	DEBUG	[uninstall]	Loaded configuration from /Library/Elastic/Agent-Development/elastic-agent.yml
2025-06-25T12:07:34.937Z	DEBUG	[uninstall]	Merged configuration from /Library/Elastic/Agent-Development/elastic-agent.yml into result
2025-06-25T12:07:34.937Z	DEBUG	[uninstall]	Merged all configuration files from [/Library/Elastic/Agent-Development/elastic-agent.yml], no external input files
2025-06-25T12:07:35.051Z	DEBUG	[uninstall]	Loaded configuration from /Library/Elastic/Agent-Development/elastic-agent.yml
2025-06-25T12:07:35.051Z	DEBUG	[uninstall]	Merged configuration from /Library/Elastic/Agent-Development/elastic-agent.yml into result
2025-06-25T12:07:35.051Z	DEBUG	[uninstall]	Merged all configuration files from [/Library/Elastic/Agent-Development/elastic-agent.yml], no external input files
2025-06-25T12:07:35.051Z	DEBUG	[uninstall.composable]	Starting controller for composable inputs
2025-06-25T12:07:35.051Z	DEBUG	[uninstall.composable]	Started controller for composable inputs
2025-06-25T12:07:35.051Z	DEBUG	[uninstall.composable]	Computing new variable state for composable inputs
2025-06-25T12:07:35.051Z	DEBUG	[uninstall.composable]	Stopping controller for composable inputs
2025-06-25T12:07:35.051Z	DEBUG	[uninstall.composable]	Stopped controller for composable inputs
Error: error uninstalling agent: error uninstalling components: error creating service components: failed to render components: invalid 'inputs.1.id', has a duplicate id "unique-system-metrics-input". Please add a unique value for the 'id' key to each input in the agent policy
For help, please see our troubleshooting guide at https://www.elastic.co/guide/en/fleet/9.1/fleet-troubleshooting.html

                                                              

[  ==] Uninstall failed  [0s] Error: failed to uninstall elastic-agent: exit status 1
For help, please see our troubleshooting guide at https://www.elastic.co/guide/en/fleet/9.1/fleet-troubleshooting.html

Workaround on MacOS

The workaround is to manually remove the daemon file and also remove the agent directory:

rm -rf /Library/Elastic/Agent-Development
rm /Library/LaunchDaemons/co.elastic.elastic-agent-Development.plist

I believe the user would need to perform similar manual steps for other OS'.

I think we should handle this scenario while uninstalling the agent.

[elasticmachine]

Pinging @elastic/elastic-agent-control-plane (Team:Elastic-Agent-Control-Plane)

[ebeahan]

@VihasMakwana what version of Agent were you running your scenarios with?

[cmacknz]

This is probably a duplicate of #3783 and we should fix this problem.

[VihasMakwana]

@VihasMakwana what version of Agent were you running your scenarios with?

Latest build from main and elastic-agent 9.0.2 downloaded from https://www.elastic.co/downloads/elastic-agent.