Handling Duplicate Filenames

On my DJI Phantom 4 Pro drone, when I run multiple missions to do 3D modeling that require multiple batteries I get multiple folders of image files that begin at image 001.  Am I correct in that when you upload these images to Pix4D cloud for processing, it treats the same filenames as duplicate files and doesn't bother to inspect the filesize or datetime stamp to see they are not duplicate files?

That seems to be what happened when I tried it and I ended up having to run the files through an auto renamer to add an incremental number to all the image filenames to make sure all filenames were unique.

I am thinking (hoping) I am missing something, or doing something wrong as running multiple missions where the filename numbers reset is a pretty common occurrence and I would be completely baffled that the Pix4D Software Designers had not taken that into consideration as that's a pretty basic consideration.

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