for specie Compartment is set by name and not compartment id when using renameCompartments and combineSubsystems functions together.

[agrimadeedwania]

some species are specified by compartment name instead of the compartment id. I have attached the image. the specie with name atc_e should have compartment as cell_external_combined

[ayush9pandey]

Thanks for putting this here. We should fix this. Do you have any further idea where in the code this might be happening and why?