Deleting data of an extension that has incorrect modules set up will cause this error to appear:

[phpBB Debug] PHP Notice: in file [ROOT]/includes/acp/acp_modules.php on line 975: Undefined index: CANNOT_REMOVE_MODULE

The migrator module tool will instantiate the acp_modules class and use the delete_module() method. However, it does not always add the language file that is required by the acp_modules class for error messages which causes this PHP notice to appear. This is especially the case when more than one module gets removed. That way, the method get_module_info() gets called first. This method will include the file for the acp_modules class without adding the language files required for error messages.