The problem is that you end up with two shelf tools that have the same name. And in Houdini session only one tool of a given name can be active.
Thanks, now I understand what is going wrong.
But I would expect that in case of conflict, it would use the tool of the current HDA. Because that behavior would automatically “deprecate” the outdated tools.
As a “fix”, I deleted the tools from the older HDA version.