By annotating your design (that is, by assigning reference designators and net names to unnamed parts and electrical connections in your design), you provide the means by which to pass it "downstream" to other layout design tools (PCB Editor, for example) that take it beyond the schematic capture phase of the design. Possible downstream applications include PCB layout tools, simulators, or logic optimizers.
If you want to preserve a reference designator during annotation, choose User Assigned Flag – Set from the pop-up menu of the part on the schematic page. You can also open the part in Properties Editor and from the pop-up menu of Reference choose User Assigned Flag – Set. The User Assigned Flag is set by the tool if the reference designator is changed using the Property Editor or Schematic Editor or through Back annotation.
Note that if the instance and occurrence values are the same in a hierarchical design, the User Assigned Flag is not set for the occurrence value. If you want to set the User Assigned Flag for the occurrence value, edit the Reference and then set the flag.
If you have placed different sections of a homogenous part like U1A, U1B, U1C in a design, and run annotation with Reset part references to ? option selected and Preserve designator option unselected, the designator information is lost in the design. To preserve designator information of a design, select Preserve Designator option in Annotate dialog box before running annotation.