I found a solution to my issue above.
Since I edited my original pictures into ‘mask images’ they still contained 3 image bands.
I removed the 2 redundant bands from the image using gdal_translate.
After this Pix4D is able to read the …_labels.png images, allowing you to import externally created masks.
However, you will still need to create the image segments individually for each image to make this work, see Create segmented image for all images .
This also means the masks will not be transferred with exact pixel accuracy, just the regions corresponding to the pix4d generated segments.
Hope this helps anyone facing the same issue.
Cheers, Brian Nieuwenhuis