This can be resolved by using patches. You will be able to manage all deployments with one overlay file per environment where you can set explicitly number of replicas for each deployment.

Here's a simplified example of it:

I have two environments: dev and stage. Both have kustomization.yaml with patches for specific deploys and numbers of replicas (different for both envs).

tree command:

.
├── base
│   ├── app-1.yaml
│   ├── app-2.yaml
│   └── kustomization.yaml
└── overlays
    ├── dev
    │   └── kustomization.yaml
    └── stage
        └── kustomization.yaml

Deployment - app-1.yaml: (2nd is almost identical, different name and image)

apiVersion: apps/v1
kind: Deployment
metadata:
  name: example-1
spec:
  template:
    spec:
      containers:
      - name: example-1
        image: example:1.0

Below a snippet from overlays/dev/kustomization.yaml:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

resources:
  - ../../base

patches:
  - patch: |-
      - op: replace
        path: /spec/replicas
        value: 2
    target:
      group: apps
      version: v1
      kind: Deployment
      name: example-1
  - patch: |-
      - op: replace
        path: /spec/replicas
        value: 3
    target:
      group: apps
      version: v1
      kind: Deployment
      name: example-2

Actual result:

$ kubectl kustomize overlays/dev
apiVersion: apps/v1
kind: Deployment
metadata:
  name: example-1
spec:
  replicas: 2
  template:
    spec:
      containers:
      - image: example:1.0
        name: example-1
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: example-2
spec:
  replicas: 3
  template:
    spec:
      containers:
      - image: example:2.0
        name: example-2

Useful links:

• Kustomize patches
• Kustomize components (this one is not directly connected, but idea is common)