This question is similar to Re-annotating hierarchical sheets but the problem I seem to be having is different.
I have a hierarchical designwhere 3 of the sheets are used twice. I have it set up that components on the duplicated sheets use a simple suffix, like _S1 and _S2 (for section 1 and 2).
Parts in the repeated hierarchy blocks end up looking like R10_S1 and R10_S2, which is fine for this as the PCB is not very dense and there's room for the long designators.
I now want to re-annotate as numbers are scattered all over the board and the first few of these I'm hand assembling. I didn't re-annotate the rev 1 boards and it was a PITA trying to find the designators. If they're numbered in some logical fashion I won't have to hunt all over...
When I do the PCB->reannotate it drops the suffix off of designators that are in the duplicated sections, i.e. instead of getting (let's say) R2_S1 and R2_S2 I get R3 and R4. I could copy the project and start some experiments to see what happens when I try and update the schematics from the PCB but I'm thinking somewhere there's an explanation of how this is supposed to be done. Google turns up the AD documents https://www.altium.com/documentation/18.0/display/ADES/((Annotating+the+Components))_AD but after reading that I'm still not clear on how to control updating the PCB so that the when back-annotated the logical designators that are represented by the schematic are done so that the physical designators on the PCB come out correctly.
If it helps visualize it here's the main schematic page where the top section (three blocks) are duplicated:
