Hello OFU_UIB,
When orthomosaic is generated PhotoScan saves not only the final orthomosaic (in tiled internal representation in several scales), but also the orthorectified original images that are projected on the surface - such files may require large disk space than the originals, if very oblique shots are used, however, more than 1 TB disk space should be sufficient.
I can suggest the following test: in the Ortho view draw the polygon that covers the hole area of reconstruction (including the missing part), then right-click on the drawn shape and choose Assign Image option. In the Assign Image dialog browse the images one by one and check if every one has orthorectified image (should be displayed in the corresponding area).