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Yes, perspectives are stored in the database, and sync just like other transactions.

One thing to note about perspectives and the iPad is that the iPad currently only supports context-mode perspectives. If you make a project-mode perspective, it will sync, but not be displayed, and the result will look just as if it hadn't synced. So, go to project mode, focus on the folder(s) in question, switch to context mode (cmd-2) and set up the grouping and sorting as you want it, then save the perspective. That should get you a working perspective on the iPad after everything syncs.

Also, on the Mac, in context mode, you can turn on a column to show the project associated with an action. View->Columns->Project. If you also sort by that, you can get a halfway decent facsimile of the project mode view (no hierarchy, but the actions should be correctly ordered, I think).