As you mentioned, it is possible to run some substeps without rerunning the whole processing Step 1, Step 2, or Step 3. For example, in the Menu > Process you can run only the generation of 3D textured mesh or only generate Conture lines without reruning the whole step.
However, in Step 3 you cannot only run the generation of the orthomosaic. When Step 3 is run the existing results are removed and both DSM and orthomosaic are regenerated.
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