3% H2O2 in my experience is not very effective when diluted in the tank, works ok poured on neat (at WC or if you can lift plants or equipment out) but can burn plants, even Anubia, if left on more than 3-5 minutes
The treatment shouldn't hurt the plants, if anything it should help them! On WC days use the recommended quantity for the whole tank to spot treat the worst areas. If you do daily WC's then you are good to go, otherwise on non-WC days I would just dose according to the Flourish Excel recommendations.