But on opening “Photos”, only the new photos imported from his phone were there.
Either way, the user got an error message, “Your Photo Library has been migrated to Photos”. Then dragged the iPhoto library in and tried to double-click it. I suspect the user created a new Photos library by importing photos from his phone. This time something strange happened, I’m not even sure what. Photos opens and automatically converts the library to a new “Photos” library. This has been seamless in the past, as you just move the iPhoto library into the Pictures folder and double-click on it. In this case an old iPhoto library from a OS X 10.9 Mavericks machine to Photos on an OS X 10.11 El Captain machine. Part of the process is transferring data, usually via target disk mode.
I ran into a weird issue the other day when switching a user to a new laptop.