I am not sure if I understood your question. You want to replace two photos and save a new 62 image panorama.
First Save as a new project. Very important.
Go to the Editor, remove the 2 photos you don't need.
Add the new 2 photos
Control points: for two photos you can add them manually (and fine tune). Running a detector will duplicate already existing points.
Now you can do it in a few ways
1. Full Align - it will change the final image proportions, exposures, possibly even the projection.
2. Optimize positions - the new images will take the place of these removed. The exposures and projection will remain unchanged. But the final image may be different.
3. Stitch the previous 62-image panorama with the 2 new photos. Mask the areas where the previous two images were.
For this operation, the 62 image panorama must be saved in 100% size.
4. If the 62 image panorama was resized to X percent of the original, resize the two photos to the same percentage.
There are many more possibilities.
For example you can open the .pto file in a text editor, replace the filenames of these 2 photos, save as a new project and open it in Hugin.
Now you should only adjust the control points, optimize and stitch a new panorama.