Do you have the right license? Are you hitting Save intensity data, or save? Also, are you closing and re-opening the SE file after you save the data? It does not appear to auto-update, so you have to re-open it. I did not delete the channels, just did not program them in the SE. I am pretty new though, so can't say for sure how you are supposed to do it, but it worked for me.
After you do File > Save Intensity Data, a new file is created. You can check for its existence.
If the SE sequence file is "MySequence.lms", then in the same directory you will find the PE sequence file "MySequence.lpe" and the intensity data file "MySequence.pe.lid".
I found the PE Prop line by using the scroll bar on the far right, it was like on the next page and not just below my last channel.