CustomResourceDefinition/helmreleases.helm.toolkit.fluxcd.io dry-run failed

[lukasdext]

Describe the bug

Hello,

I'd like to request assistance with a persistent issue I'm facing with Flux CD in a critical production environment running on AWS EKS. Due to the nature of the environment, re-bootstrapping or starting the installation from scratch is not an option.

The core problem is a Kustomization that is constantly failing with a CRD validation error: status.storedVersions... Invalid value: "v2": must appear in spec.versions.

I have followed documentation and suggestions to resolve this by manually editing the CRD (kubectl edit crd...) to remove the stale v2 entry from the status.storedVersions field. However, the problem persists because the Flux controller reverts my manual changes as soon as I resume the Kustomization, reapplying the old, invalid CRD definition from our Git repository.

Could you please provide guidance on the correct procedure to permanently fix the CRD definition from our Git repository and resolve this reconciliation loop safely?

flux get kustomizations fluxcd --namespace=fluxcd
NAME REVISION SUSPENDED READY MESSAGE

fluxcd main@sha1: False False CustomResourceDefinition/helmreleases.helm.toolkit.fluxcd.io dry-run failed, reason: Invalid: CustomResourceDefinition.apiext
ensions.k8s.io "helmreleases.helm.toolkit.fluxcd.io" is invalid: status.storedVersions[0]: Invalid value: "v2": must appear in spec.versions

Steps to reproduce

flux get kustomizations fluxcd --namespace=fluxcd

flux reconcile kustomization fluxcd --namespace fluxcd

Expected behavior

flux reconcile kustomization fluxcd --namespace fluxcd

success

Screenshots and recordings

No response

OS / Distro

windows

Flux version

PS C:\Users\lukas\Downloads\JB> flux version -n fluxcd flux: v2.6.4 distribution: flux-v2.1.1 helm-controller: v0.36.1 image-automation-controller: v0.36.1 image-reflector-controller: v0.30.0 kustomize-controller: v1.1.0 notification-controller: v1.1.0 source-controller: v1.1.1

Flux check

PS C:\Users\lukas\Downloads\JB> flux check -n fluxcd
► checking prerequisites
✗ Kubernetes version v1.30.13-eks-5d4a308 does not match >=1.31.0-0
► checking version in cluster
✔ distribution: flux-v2.1.1
✔ bootstrapped: true
► checking controllers
✔ helm-controller: deployment ready
► ghcr.io/fluxcd/helm-controller:v0.36.1
✔ image-automation-controller: deployment ready
► ghcr.io/fluxcd/image-automation-controller:v0.36.1
✔ image-reflector-controller: deployment ready
► ghcr.io/fluxcd/image-reflector-controller:v0.30.0
✔ kustomize-controller: deployment ready
► ghcr.io/fluxcd/kustomize-controller:v1.1.0
✔ notification-controller: deployment ready
► ghcr.io/fluxcd/notification-controller:v1.1.0
✔ source-controller: deployment ready
► ghcr.io/fluxcd/source-controller:v1.1.1
► checking crds
✔ alerts.notification.toolkit.fluxcd.io/v1beta2
✔ buckets.source.toolkit.fluxcd.io/v1beta2
✔ gitrepositories.source.toolkit.fluxcd.io/v1
✔ helmcharts.source.toolkit.fluxcd.io/v1beta2
✔ helmreleases.helm.toolkit.fluxcd.io/v2
✔ helmrepositories.source.toolkit.fluxcd.io/v1beta2
✔ imagepolicies.image.toolkit.fluxcd.io/v1beta2
✔ imagerepositories.image.toolkit.fluxcd.io/v1beta2
✔ imageupdateautomations.image.toolkit.fluxcd.io/v1beta1
✔ kustomizations.kustomize.toolkit.fluxcd.io/v1
✔ ocirepositories.source.toolkit.fluxcd.io/v1beta2
✔ providers.notification.toolkit.fluxcd.io/v1beta2
✔ receivers.notification.toolkit.fluxcd.io/v1
✗ check failed

Git provider

github

Container Registry provider

ecr

Additional context

Hello,

I'd like to request assistance with a persistent issue I'm facing with Flux CD in a critical production environment running on AWS EKS. Due to the nature of the environment, re-bootstrapping or starting the installation from scratch is not an option.

The core problem is a Kustomization that is constantly failing with a CRD validation error: status.storedVersions... Invalid value: "v2": must appear in spec.versions.

I have followed documentation and suggestions to resolve this by manually editing the CRD (kubectl edit crd...) to remove the stale v2 entry from the status.storedVersions field. However, the problem persists because the Flux controller reverts my manual changes as soon as I resume the Kustomization, reapplying the old, invalid CRD definition from our Git repository.

Could you please provide guidance on the correct procedure to permanently fix the CRD definition from our Git repository and resolve this reconciliation loop safely?

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