There is not a simple way to make such changes in the current HMC implementation.
HMC manage nodes configuration by using Puppet in the background, so any change done outside of HMC (manually) reverted back to HMC known configuration.
There are a simple workaround in here: do not use HMC to restart mapreduce if you made changes in its configuration. Just use scripts to stop and start mapreduce services.
This behavior suppose to be changed in future implementations, however, there is not a definitive timeline for this changes yet.
Hope this helps!