The detached-shell source R Scl, displaying CO emission from recent mass loss, in a binary-induced spiral structure as well as in a clumpy shell produced during a thermal pulse, provides a unique laboratory for studying the differences in CO isotope abundances throughout its recent evolution. We observed both the ^12^CO(J=3-2) and the ^13^CO(J=3-2) line using ALMA. We find significant variations in the ^12^CO/^13^CO intensity ratios and consequently in the abundance ratios. The average CO isotope abundance ratio is at least a factor three lower in the shell (~19) than that in the present-day (<~300yr) mass loss (>60). Additionally, variations in the ratio of more than an order of magnitude are found in the shell itself. We attribute these variations to the competition between selective dissociation and isotope fractionation in the shell, of which large parts cannot be warmer than ~35K. However, we also find that the ^12^CO/^13^CO ratio in the present-day mass loss is significantly higher than the ^12^C/^13^C ratio determined in the stellar photosphere from molecular tracers (~19). The origin of this discrepancy is still unclear, but we speculate that it is due to an embedded source of UV-radiation that is primarily photo-dissociating ^13^CO. This radiation source could be the hitherto hidden companion. Alternatively, the UV-radiation could originate from an active chromosphere of R Scl itself. Our results indicate that caution should be taken when directly relating the ^12^CO/^13^CO intensity and ^12^C/^13^C abundance ratios for specific asymptotic giant branch stars, in particular binaries or stars that display signs of chromospheric stellar activity.