This misleading error message refers to changing the version of the Sencha Cmd tool on the computer you are using. You can upgrade the Cmd scaffolding with the following command:
sencha app upgrade --noframework
From: 'sencha help app upgrade'
Options * --noframework, -no - Upgrade only the Sencha Cmd scaffolding and not the SDK
Definitely back up your application before upgrading. The update team will warn you of conflicts that need to be resolved (for example, user changes in app.js). When you open these files, the differences will be noted in the standard diff format:
<<<<<<< Generated /* This file is generated and updated by Sencha Cmd. You can edit this file as needed for your application, but these edits will have to be merged by Sencha Cmd when it performs code generation tasks such as generating new models, controllers or views and when running "sencha app upgrade". Ideally changes to this file would be limited and most work would be done in other places (such as Controllers). If Sencha Cmd cannot merge your changes and its generated code, it will produce a "merge conflict" that you will need to resolve manually. */ ... >>>>>>> Custom ...
Eliminate the conflicts (delete → → → the lines of X and make sure that the correct lines are included in your file), and you should be configured. The most likely file for conflict is app.js - it would be nice to compare your backup version of this file with your modified version to be sure of the changes.
This means that all developers working in the application must run the same version of Cmd, so keep that in mind.
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