The input impedance of the Mic inputs is lower than the line inputs. In addition, the Mic Inputs have DC blocking capacitors that the line inputs do not have.
If the output impedance of the line-level source is low (as it should be with modern gear), then the difference in input impedance should not make any real difference in the sound.
The DC blocking cap adds a high-pass filter (that's the point -- to block the DC phantom voltage); the corner frequency of this filter is very low (a few hertz) so it will not have any effect on the frequency response, but it does introduce a frequency sensitive phase shift, that may (or may not) have some impact on the timbre of the sound (it will be very dependent of on the nature of the audio).
The line input path is going to be the most transparent for a line-level signal. But the Mic Input path is almost as transparent.
For most sources, it is unlikely that you will be able to tell the difference, but there are some sources that you will be able to distinguish the input paths.