When you import a stereo sample, it gets divided into 2 separated samples configured to be both channels left and right.
If you re-import the samples and ask for replace, you expect that the left channel replaces the left channel and the right channel replaces the right channel and that all the configurations made on the samples, i.e., tuning and loop settings, are kept.
What happens instead: when you re-import a stereo sample and ask for replace, both channels (left and right) are replaced by one channel, so the sample gets mono. And all the configuration gets lost!