Sometimes the ideal colours for your project are reactive with each other, but a reaction line, or area, is undesirable.
Bob Leatherbarrow has demonstrated the possibility of avoiding the reaction. This works most clearly when using frit to blend one colour into another. Lay down the first reactive colour, then add clear frit or powder to cover the overlap area before adding the second reactive colour. The clear separates the two, but does not interfere with the transition or blending because the two colours cannot interact.
It is less easy with sheets of glass where you want to avoid a reaction line. In these cases you want to have a small but consistent gap between the reactive pieces. Place the glass with the gap and fill it with clear powder or fine frit to inhibit the reaction. You will need some experimentation to determine the necessary space between the glasses to avoid the reaction line without allowing a lot of light through, or the base glass showing as a line instead of the reaction line. After this you may decide that the reaction line is not so bad anyway!