Hi John,
MQ will not delete or modify content in the userdata folder unless you delete the queue manager. You can use it for whatever you need to, including template configuration files. This folder was specifically created to provide a place for user files and other state that needs to be replicated between nodes. Content in the folder will consume capacity from the RDQM queue manager file system, but a few small configuration files should have minimal impact. For larger amounts of data, its size will need to be considered when allocating the queue manager file system.
Kind regards,
Jamie