Altium - Back-Annotation Error
Go figure, I struggle with this for two hours and as soon as I finally post the question I manage to figure it out.

Apparently in one of Altium's latest updates either the functionality changed or a setting was changed. For some reason I am not able to update schematic designators unless their respective components are selected. In the case of the above problem only a few of the schematic designators were selected when I attempted the back-annotation, so to the annotation tool the number of components on the PCB that were re-annotated and the number of components selected in the schematic did not match. I had to select all of the components in the schematic in order to perform back-annotation.

Seems a bit ridiculous to me, so if anyone knows if there is a setting to change this, please let me know. Regardless, the solution mentioned above worked for me.