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Merging projects results in displacement of courtyard

So I have a large project for a building where we had done multiple flights to capture all the sides of the walls with the phantom 4 pro. to save processing time we split up the projects in to sub projects. When we initial did the flight we did not have any way of recording GCPs at that time. Recently we went out and captured an overhead scan with gcps and were planning on using this new flight to merge with all the other projects. I did a quick test to see if I would have any problems tying the data together and got some interesting results.

As you can see, the south side of the building merged with the overhead completely fine, in fact it was only a little out of position but I was able to align the data with manual tie points.

The real problem I’m having is with the one courtyard I included. when I initially created the merged project, it was above the scan to a large degree. using the basic tie point editor I was able to create some manual tie points between the overhead and the courtyard dataset and was able to bring it down to this level where it is currently at. I cant get it to go down further past this.

Has anyone encountered this or know of quick solutions to try?

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