Thanks @Thiseas C. Lamnidis . So the first option you describe would be to set same library name for al subset chunks, but set lanes 1,2..N?

you would be setting the library name of each run so it includes the lane number (or whatever unique ID). That would indeed set the LB in your bam headers to the “wrong” thing, but that can be fixed by reheading the final BAM before providing them to eager as a BAM input for the second run