Multiple blocks indicate that there were not enough matches between the different blocks to provide a global optimization. The different blocks might not be perfectly georeferenced with respect to each other.
Adding Manual Tie Points between the blocks and reoptimizing can connect the blocks together. By marking a point in several images, we indicate that certain point should be reprojected as closer as possible in the 3D model, considering all the images reprojections. For more information: https://support.pix4d.com/hc/en-us/articles/202560349
Additionally, enabling the option Rematch may improve the connection between the blocks. For more information about the Rematch option: https://support.pix4d.com/hc/en-us/articles/205327965#label5
Before merging the sub-projects, could you confirm you added MTPs or GCPs to make the connection between the different subsets of images?
For more information about processing large datasets: https://support.pix4d.com/hc/en-us/articles/202558579