I just had this same problem, but solved it like so:
In your project window, expand the Dependencies group. You should see each of the undesired subvi's listed there.
Right click on each one and select 'Replace with item found by project...'. This will bring up the familiar conflict resolution dialog box, go ahead and select the proper path and click OK.
Now, because the dependency has changed, Labview is going to change the dependency path that is saved in the calling VI. You'll see a save dialog asking if you want to save the changes to the VI(s) that is/are calling the dependency whose path you just changed. You want to save changes.
Do this for all the dependencies and you should be good to go.