I have some png files that I am applying a color to. The color changes depending on a user selection. I change the color via 3 RGB values set from another method. The png
Have you looked at the functions available in Bitmap? Something like extractAlpha sounds like it might be useful. You an also look at the way functions like that are implemented in Android to see how you could adapt it to your particular case, if it doesn't exactly meet your needs.
The answer that worked for me was a write up Square did here Transparent jpegs
They provide a faster code snippet for doing this exact thing. I tried extractAlpha and it didn't work but Square's solution did. Just modify their solution to instead modify the color bit and not the alpha bit.
i.e.
pixels[x] = (pixels[x] & 0xFF000000) | (color & 0x00FFFFFF);