According to the Season Challenge Q&A, the boosts works for all upgrades in progress. The players just need to quit the n restart the game, the building/research time should have been shortened. But I never find it works actually when my boosts have been increased from 10% to 15%, or from 15% to 20%. Nevertheless, for new upgrades, there was really discount in both cost n time. It just not works for upgrades in progress.

I hope that Supercell can fix the bug asap.