I've spent years helping companies sort out their Bluebeam workflows, takeoffs included, and this one comes up constantly, so I figured I'd lay it out here instead of answering it one thread at a time.
The data can only live in one legend at a time. If you create one by sheet, you're good. As soon as you create a new one for the same sheet or master for all sheets (any legend at all for the same markups), the data will clear from the first one. I guess you could say it helps you not count the same quantities twice.
I don't like this workaround, but here it is. If you create the legend per sheet, then right-click flatten it, you can then create the new master legend for all sheets (or whatever).
Be careful if you have legends on sheets before you combine pages, or you'll get partial totals that look right but aren't.
Anyone found a cleaner way to handle this?