I've noticed that when I select multiple tracks (usually, but not always, an entire album) and then send them to the format converter, the converted files are no longer selected.
This makes sense because they're not the same files.
This doesn't make sense because they are the same "track" and occupy the same role (playlist inclusion, etc) in the library as they did before the conversion.
I don't know what the "right" answer is for this, but almost all of the time I find myself wishing the tracks were still selected (I usually either reorganize them at this point and/or add them to the library and/or scan for volume analysis). This is especially true when they are non-contiguous files in a longer list, because I then have to hunt each one down and re-select it for further processing.