I've read that modifying the bin values in the frequency domain after a FFT poses problems that lead to glitches when one takes the signal back to time domain using iFFT. This is caused iirc because the modified data does not align "continuously" anymore to the bins (and discontinuities $\implies$ artefacts). Because of this it's e.g. not recommended to perform ("ideal filter") equalisation in the frequency domain.
But since there are e.g. interpolation methods,
Are there ways for doing processing such as shuffling or removing bins in the frequency domain such that one can retain sound quality? E.g. by "synthesising" new data using interpolation methods.
In the context of audio something seems to be feasible, since there exists plug-ins such as this that seem to do filtering in the frequency domain: