How can I change the affected/unaffected status of a sample to run new algorithmic filters?

It is possible to change the affected status of the merged analysis from the three horizontal lines next to the analysis name on the Analyses page.

This option is useful in order to run algorithmic filters for segregating variants, where you need to set which sample is the affected and unaffected respectively. 

You will be directed to a screen, as the one shown below:

You can delete the filters displayed, then update the affected/unaffected status of your samples and run the algorithmic filters you would like for your merged analysis.