The following provides a method of cleaning out unwanted bundles from SDDC Manager. Firstly browse to the Bundle section on SDDC UI, select the bundle you wish to remove and click view details:

From here you can gather the Bundle ID which is required by the bundle cleanup utility:

At this point it is good practice to take a snapshot of the SDDC Manager VM. Next SSH to the SDDC Manager VM and elevate to root user. Followed by running the bundle cleanup utility:

python /opt/vmware/vcf/lcm/lcm-app/bin/bundle_cleanup.py <bundle id>

Finally run a restart of the lcm service and use curl command to check if service online:

systemctl restart lcm

curl localhost/lcm/about | json_pp

Confirm in the SDDC UI that the bundle is no longer present!