Hello @StephenWick,
It seems that the other workaround would not work in these versions. We apologize for the confusion.
Looking at the Welcome_CW_MCUs text document in CWMCUV61RN it mentions the following:

[Welcome_CW_MCUs -> General Limitations]
Could you please try the above workaround in case you are using MC8S08QE?
Also, in the CodeWarrior Developoment Studio IDE 5.9 User’s Guide there is a section about Program/Verify (check Figure 23-4. Program/Verify Panel) where is mentioned the possibility of change the address range to program flash data. Could you please take a look at it?
If none of the above works or is useful, as @guriinas23 mentioned it might be necessary to "create a new project in CodeWarrior 5.9.0 and import the source files and settings from your old project into the new one. This process can sometimes help update the project to the newer format."
Best regards, Raul.