Can you please not overwrite the DSM data when processing the DTM data? If someone wants an orthomosaic, that should remain when creating a DTM and resulting datasets. All the DTM files should be written to their own folder, separate from the DSM data.
In the latest version of Pix4Dmapper, when a DTM is created after running the Classification Tool, a new folder called dtm is created in 3_dsm_ortho where the DTM is stored. It therefore does not overwrite the DSM which is in 1_dsm.
Restarting the 3rd step of processing or exporting a modified orthomosaic in the Orthomosaic Editor would both overwrite a previously outputted orthomosaic. As such, it is often a good idea to make a copy of the DSM, especially if creating it was a time consuming process.