Huh, so is that a schematic compile warning?
Because the compiler doesn't take account of the annotation file. If you have e.g. R10 in a channel that's numbered $ComponentPrefix$ChannelIndex$ComponentIndex (so its instances will be named "R110", "R210", etc.), and you have R110 elsewhere in the schematic, then the schematic annotation won't detect any issues (because there is only one part with logical name "R110"), but the compiler will emit a warning, because there are multiple physical parts (R110 by name, and "R110" from channel 1, "R210" from channel 2, etc.).
That is an issue if you are doing simulations (the compiled designators are used for simulation). It doesn't matter on the PCB, because the PCB does use the annotation file.
At least, I think that's what it does. Again, good reasons to avoid using confusing names and back annotation...
Tim