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Is there a way to automatically change all classes with Persistent and Shared Transient lifetimes disabled to Transients Only?

Not that I'm aware of, but have you actually run out of class numbers, or getting close to running out of class numbers?

If not, personally I'd wait until you actually need to utilise additional class numbers before changing any classes to use the Transients Only option due to the following comment from Jade Support Bulletin #12.

There are some runtime restrictions and performance ramifications associated with using this feature.

Ref: https://forums.jadeworld.com/viewtopic.php?f=24&t=1798

Cheers,
BeeJay.

You could try doing a schema extract and updating the schema file (*.scm) and then reloading it. (Suggest you try this in a test system first and don't make changes in Jade before reloading.) The format's not too difficult, if you still have Jade 5.2 documentation then, Jade lists the format of the schema files in the Object Manager or Developers reference as an appendix. Otherwise, you should be able to work it out by extracting a class of each type.