Assuming (from peeking at previous posts) that you have the professional version of metashape, you can add markers without coordinates to align the chunks, if you can see common features in at least two aligned photos in each chunk.
If you can't, then that would explain why the photos don't align, and I don't see any other 'workaround' as it implies that there is no overlap between the chunks, or no way to match overlapping areas if there are any.
If you can, then you need to add at least 3 well distributed markers to each pair of chunks, with the same names in each chunk, and use the marker based option for aligning chunks.