Hi John,
If I understand you correctly, the problem is that all data lines in a sample get the same flags if I do it the way I described: in Analyze, click to select samples in specific order, open Elements/Cations, click OK to assign Elements/Cations settings of first selected sample to all selected samples.
For us that would be fine. Yes, I can edit these settings individually for each line in Run | Display Multi Background Intensities. But for everything else, i.e. all the processing settings in Analyze!, Calculation Options, TDI settings..., lines in a sample are treated the same anyway, right? So if I want to use different settings for any of these, I either have to create separate samples for acquisition, which is what we tell our users to do. Or, if they haven't done that, save different versions of the file with different settings for the sample and use the lines from different files.
I would assume if anyone uses different multi-point background settings for different lines in a sample they would have set that up manually anyway, so they wouldn't need to apply a different setup to this sample?