Annotate Reference Designators from a Text File

One method is to use Schematic Editor > Tools > Annotate > Back Annotate Schematics and load in a Was-Is file. The Was-Is file is simply a text file with the current designator a space (not tabs) and the new designator on each line.

C1 C4
C2 C3
C3 C2
C4 C1

The file name has a .was extension.
This will change both the schematic and the PCB designators, not just the PCB designators.
Copy / pasting from Excel to a text editor works but you will have to change all the delimiters from tabs to spaces. 

If you want to change only the PCB side then paste into the string column of the designators in the PCB List panel and re-link components by designator should work.

Source: 

Annotate Reference Designators from a text file? - Altium Discussion Forums - Eric Albach

That's it ! 

Update Schematic from Library

Altium BugCrunch #839 : 

 Position of refdes after update from library.

1. Open SCH List Panel. Select All Objects > Include only Parts. 
2. Copy current Orientation, and Mirror-status to a spreadsheet.
3. Set to 0 and non-mirrored. 
4. Perform library update.
5. Copy spreadsheet data over SCH List data to recover original positions.

'via Blog this'

Add Move Text to Edit Menu

Add Text to the Move menu to simplify working with silkscreen and assembly drawings.

Right Click on Main menu bar > Customize > New

Then create the Command and select Ok

Click to view image

Then drag the new Text Command into the main menu > Edit > Move

Move > Text

Setup and Using layer pairs - YouTube

Setup and Using layer pairs - YouTube By Microdex:

This video includes creating a Layer Pair for Assembly Drawings that use '.designator' on a mechanical layer.

Key points include defining the Layer Pairs while all placed parts are on the Top Layer.