Currently, if you perform a Re-import or Re-score operation and then press the cancel button in the progress graph view, Skyline drops all of the replicates it has not gotten to yet, with the negative consequences of dropping any manual integration or annotations on these.

We should at least ask whether to Re-import in place or save as, like we do for Re-score and minimize. Better still might be to just keep around the original .skyd file, and just restore the data from any replicates we do not make it to by the time the user presses the cancel button.