added the modifications for the multiple demultiplexing case

Sverker noted that you can't edit again steps marked as done. As such, when you mark reads as "To be included in the total", that decision is final, and shouldn't be. The modifications causes the total to be only calculated from the latest demultiplexing happened on a given flowcell+lane.
I don't have any major objections to merging this once you get the go-ahead. This repo is **not** in my wheelhouse, but the only remark I can make is:

Please remove commented-out code. It's just distracting.