i've been sewing/quilting for many years now...i've used what ever thread is right there...over and over, if the color is ok...and it is not breaking constantly i use it, i do not pay any attention to what the last spool i emptied was i just start again with the next one...i've never had a problem with different threads in a project...i've only had problems with some threads breaking alot in my machine and problems with invisible threads...which i hate using...beyond that i don't (sweat the small stuff)
i do tend to do my hand applique and piecing with silk thread but that is just a personal choice, i just love hand work with silk thread, it is so smooth and easy to use....but if i run out and have to use cotton, or rayon or polyester i don't worry about it....too many other things in life to worry about -- ;)