For other users interested in this issue and the solution here is a part of my direct conversation with Kambiz
"I investigated all the files you sent us. Indeed, the software had a problem with merging tiles of DSM. As a result, a part of the output is missing. Please look at the screenshot below which shows part of the log file with the registered issue. As the DSM was not appropriately generated, other data which are made based on DSM are also corrupted. It is not known why it situation took place. One reason I can come with it was a RAM issue. Therefore please do the following test:
- The first fix I would recommend is to slightly lower the hardware resources, as shown in the image below. Reduce the number of cores to ensure that Pix4D is not consuming more resources than your system is capable of sustaining. It can prevent the system from crashes and other weird behaviours.
- Reprocess, Step 3. However, please unselect the generation of other outputs so we could focus only on DSM and save time as the project is quite large."
It resolved the problem.
Thank you, Kambiz for your cooperation ;-)