Process each subproject using the processing options that are most appropriate for each subproject, independently.
For example, if a project area is captured using both oblique and nadir imagery, process the oblique subproject using the 3D Models processing template and nadir subproject using the 3D Maps processing template, or apply comparable processing options.
For step by step instructions about how to merge projects: Merging projects.
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I've found that if you are merging large data sets and experience crashing or extremely large merging times, it is helpful to uncheck the "Generate Orthomosaic Preview in Quality Report" on each sub-project. While adding manual tie points will help two separated appear to be one, the rematch and optimize should be run to get a quality merge. It takes a ton of time on larger projects but is better than telling your client that your data is junk (or even worse, your client telling you that your data is junk).
Thank you for posting your processing hints regarding merging project under this article. Now all users can take advantage of it.