Converting an input audio file to a monophonic FLAC file
I think your code would become much simpler and more readable if you encapsulated all the BASS-related functionality from into separate types.

Something like:

class Stream
{
    private readonly int handle;

    // add overload that supports setting offset and lenght, if you need that
    public Stream(string inputFile, BASSFlag flags)
    {
        handle = BASS_StreamCreateFile(inputFile, 0, 0, flags);

        if (handle == 0)
            throw new BassException("Could not create stream");
    }

    public ChannelInfo GetInfo()
    {
        var result = Bass.BASS_ChannelGetInfo(stream);

        if (result == null)
            throw new BassException("Could not retrieve stream info");

        return result;
    }

    // etc.
}


This would simplify the start of your code to just:

Stream stream = new Stream(inputFile,
    BASSFlag.BASS_STREAM_DECODE | BASSFlag.BASS_SAMPLE_FLOAT | BASSFlag.BASS_STREAM_PRESCAN);
var info = stream.GetInfo();