Hi @Nina Gallavan ,
Unfortunately , we cannot use powershell to merge the two sets of Term Store.
So far you can only manually select the Merge term to achieve your needs.
Reference: https://learn.microsoft.com/en-us/sharepoint/create-and-manage-terms
Note that the term that you merge with needs to be on the same hierarchical level, so if the term that you want to merge with is child to another term, you first need to move the source term to the same parent.
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