Electronic – Altium: Using Find similar object to change all designator fonts at once

To clear the selection of the Find Similar Objects use the SHIFT + C hotkey.

After performing the edit, you will probably find that all the other objects on the schematic are faded out, or masked. While something is masked it cannot be edited, to remove the mask click the Clear button at the bottom right of the workspace [shortcut: SHIFT + C]. Page 4

And as for the footprint changes, I think the Footprint Manager is what you need.

Altium Designer's schematic editor includes a powerful Footprint Manager. Launched from the Schematic Editor's Tools menu (Tools » Footprint Manager), the Footprint Manager lets you review all the footprints associated with every component in the entire project. Multi-select support makes it easy to edit the footprint assignment for multiple components, change how the footprint is linked, or change the Current footprint assignment for components that have multiple footprints assigned. Design changes are applied through Altium Designer's standard ECO system, updating both the schematic and the PCB if required. Page 12

You can do this via Tools -> Board Level Annotate.

You will need to select $ComponentPrefix$GlobalIndex in the "Annotate Options" screen.

However, this is uncommon for Altium and "Copy room format" might behave erratically, so I wouldn't recommend it.

You can always set custom designators for your physical components. To do this, you will need to compile your schematic (c->r) and in the bottom of your schematic you will then see the name of your compiled sheet, eg. U_IO1, U_IO2, ... Switch to one specific sheet and then double click the designator. This will give you the "Physical Component Properties" screen where you can assign a designator manually as well. Again, not really recommended.