a short-answer question:
I have used a same metadata file for my all libraries (the IDs are same)! When I want to merge the ref-seq and tables, the libraries columns’ name would be same consequently, so it should not be happened! This is my fault!
I am looking for a way to update the ref-seqs and tables with the modified metadata files (different ID with others)! otherwise they will be mixed after merging then I will not be able to separate them! Is there any way? or I have to begin from scratch?