Colour balancing of data that was filtered by a light pollution filter is fundamentally impossible; narrow (or wider) bands of the spectrum are missing and no amount of colour balancing is going to bring them back and achieve proper colouring. A typical filtered data set will show a distinct lack in yellow and some green when properly colour balanced. It's by no means the end of the world - it's just something to be mindful of.
Correct colouring may be achieved however by shooting deep luminance data with light pollution filter in place, while shooting colour data without filter in place, after which both are processed separately and finally combined. Colour data is much more forgiving in terms of quality of signal and noise; the human eye is much more sensitive to noise in the luminance data that it is in the colour data. By making clever use of that fact and performing some trivial light pollution removal in Wipe, the best of both worlds can be achieved.
You can convert everything you see to a format you find convenient. Give it a try!