Output of helm version: version.BuildInfo{Version:"v3.0.0-rc.3", GitCommit:"2ed206799b451830c68bff30af2a52879b8b937a", GitTreeState:"clean", GoVersion:"go1.13.4"}

Output of kubectl version:
Client Version: version.Info{Major:"1", Minor:"15", GitVersion:"v1.15.1", GitCommit:"4485c6f18cee9a5d3c3b4e523bd27972b1b53892", GitTreeState:"clean", BuildDate:"2019-07-18T09:18:22Z", GoVersion:"go1.12.5", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"15", GitVersion:"v1.15.3", GitCommit:"2d3c76f9091b6bec110a5e63777c332469e0cba2", GitTreeState:"clean", BuildDate:"2019-08-19T11:05:50Z", GoVersion:"go1.12.9", Compiler:"gc", Platform:"linux/amd64"}

Cloud Provider/Platform (AKS, GKE, Minikube etc.):
DigitalOcean

Premise

When creating a new chart, and then attempting to apply values using either --set or via a file (-f values.yaml), the new values will not apply if there have been no user supplied values.

Detailed logs

These have been reproducable for the at least rc-2 and rc-3. Multiple times, and in both the default and other namespaces. For example, I am using the stable/redis chart; although, any chart appears to have this issue, including file-based charts.

$ helm install redis stable/redis
....

$ helm upgrade redis stable/redis --reuse-values --set a=a
Release "redis" has been upgraded. Happy Helming!
NAME: redis
LAST DEPLOYED: Wed Nov  6 21:54:07 2019
NAMESPACE: default
STATUS: deployed
REVISION: 2
TEST SUITE: None
NOTES:
...

$ helm get values redis
USER-SUPPLIED VALUES:
null

Notice how there is nothing coming back, when we expected

USER-SUPPLIED VALUES:
a: a

Instead, it appears that we must first omit --reuse-values the first time we modify the chart.

$ helm upgrade redis stable/redis --set a=a

$ helm get values redis
USER-SUPPLIED VALUES:
a: a

$ helm upgrade redis stable/redis --reuse-values --set b=b
...

$ helm get values redis
USER-SUPPLIED VALUES:
a: a
b: b

$ helm upgrade redis stable/redis --reuse-values --set a=c
...

$ helm get values redis
USER-SUPPLIED VALUES:
a: c
b: b