If you open the metamodel and add new prolog rule, then close the file and open it again, the rules disapear. It is enough however, to move anything within metamodel and then save it to also save the prolog rules.
The only way I can get around this bug is by clicking "Save As..." from the main menu since you aren't able to directly save the current model. It seems as if changing a constraint doesn't register as "changing" the model.
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The only way I can get around this bug is by clicking "Save As..." from the main menu since you aren't able to directly save the current model. It seems as if changing a constraint doesn't register as "changing" the model.