Endolith's recent question on zeroing FFT bins got me thinking about a possible error in my workflow and I'd like to double check.
Consider a signal $x_i[m],\ m\in\{1,\ldots,M\}$, i.e. $M$ samples sampled at $f_s$ and the subscript denotes the $i^{th}$ such signal segment. I then filter this with a bandpass filter to between $0.1 f_s$ and $0.3f_s$ (at this stage, I was careful to not do a zero-the-bins kind of filtering) and Fourier transform it with an $N>2M$ long FFT. Let $X_i[k],\ k\in\{0,\ldots,N-1\}$ denote the Fourier coefficients and the filtered portion (including the roll-off frequencies on both ends) be the indices $0< k_l,...,k_u< N-1$.
My application now involves applying some function, $g$ to the Fourier coefficients $X_i[k_l],\ldots,X_i[k_u]$, averaging across the different segments ($i$) and inverse Fourier transforming the resulting vector. In math, I compute
$$X_{avg}[k]=\left\langle g(X_i[k])\right\rangle_i,\ k\in\{k_l,\ldots,k_u\}$$
where $\langle\cdot\rangle_i$ denotes averaging over the different segments. So far, so good.
Now, I didn't know what to do with the remaining Fourier coefficients $X_i[k'],\ k'\in\{0,\ldots,N-1\}\backslash \{k_l,\ldots,k_u\}$ before taking the IFFT. These coefficients are theoretically insignificant, since I've already filtered out content in them. So I went ahead and set $X_{avg}[k']=0$ and then computed the IFFT of $X_{avg}$. The results were along the lines of what I expected, but I didn't think of the aforementioned filtering issue, although I was aware of it (this is the same situation, with a bit of twists at places).
My question then is: Is it still a problem in this case i.e., when the bins that I "zeroed out" were technically low/insignificant? If so, how should I have handled it?