Notes:
--------
1) Cloud Foundry app used for verification
$ cat cf-nodejs-app.yaml
name: cf-nodejs
lifecycle: cnb
buildpacks:
  - docker://my-registry-a.corp/nodejs
  - docker://my-registry-b.corp/dynatrace
memory: 512M
instances: 1
random-route: true
2) I have attached the Helm chart used for k8s manifest generation

Reproducer:
------------
R1) Discover the above Cloud Foundry app
./kantra discover cloud-foundry --input=./cf-nodejs-app.yaml --output-dir=./discovery/
$cat ./discovery/discover_manifest_cf-nodejs.yaml
name: cf-nodejs
randomRoute: true
timeout: 60
buildPacks:
    - docker://my-registry-a.corp/nodejs
    - docker://my-registry-b.corp/dynatrace
memory: 512M
instances: 1
lifecycle: cnb

R2) Remove key/value pair(s) in the discovered manifest file and define the removed value/key pair in the values.yaml file in 
    the Helm template used for k8s manifest generation 

$ cp ./discovery/discover_manifest_cf-nodejs.yaml ./discovery/modified_discovered_manifest.yaml
$ cat ./discovery/modified_discovered_manifest.yaml (Removed timeout and instances keys)
name: cf-nodejs
randomRoute: true
buildPacks:
    - docker://my-registry-a.corp/nodejs
    - docker://my-registry-b.corp/dynatrace
memory: 512M
lifecycle: cnb

$ cat helm_sample/values.yaml 
data:
  timeout: "120"
  instances: "2"

R3) Generate k8s manifest 
./kantra generate helm --chart-dir=/home/nachandr/mta73_cli/helm_sample --input ./discovery/modified_discovered_manifest.yaml
---
# Source: helm_sample/templates/configmap.yaml
apiVersion: v1
kind: ConfigMap
metadata:
  name: cf-nodejs-config
data:
  RANDOM_ROUTE: true
  TIMEOUT: "120"
  BUILD_PACKS: |
    - docker://my-registry-a.corp/nodejs
    - docker://my-registry-b.corp/dynatrace
  INSTANCES: "2"
---
# Source: helm_sample/files/konveyor/Dockerfile
FROM busybox:latest

RUN echo "Hello cf-nodejs!"

---------------------------------------------------------
After fix,
The missing key/value pairs from the discovered manifest got picked from the values.yaml file in the Helm chart.