Command references for the "Execute Another Command" action's "Execute selected command" option are only maintained if the referenced command is imported as part of the same profile as the referencing command.
E.G. if you have "Command A" referencing "Command B" using the "Execute selected command" option, both "Command A" and "Command B" need to be part of the same profile, exported together to the same .vap, and imported together, in order for the reference to remain valid.