The constraint change doesn't work when data is filtered. It works though when unfiltered, then select several rows of data, but it is a bit inconvenient to do that rather than filter."
This is right, you can't generate a cost-benefit chart/apply resource constraints with filters. This unfortunately is a limitation with Excel and nothing we can do about.
Here is a way to do it:
Highlight the alternatives you want excluded
Right-mouse click > Exclude Alternative (this will automatically re-prioritize)
Sort Alternatives (so all the excluded alternatives fall to the bottom)
Generate the cost-benefit charts/apply constraints
Right-mouse click > Include All Alternatives (to bring them back)
This is somewhat made easier if you're taking all projects from, e.g. one of the initiatives:
Apply Filters to Alternatives
Sort Ascending or (Custom...) then apply the custom options
Go to step 1 above (Highlight...)
The reason for the message is so people don't filter, and then assume the cost-benefit would be based on the filtered results.
Another and maybe more preferable solution is to hide the alternatives. This will both exclude them from the view, the cost-benefit chart and the constraints. However, make sure you use the "Hide Alternatives: and "Unhide All Alternatives" buttons on the toolbar. Do not use the Hide/Unhide rows from the Excel menu.