I know that the Degreaser decreases its afterburn damage by 25%, but what about if I have the Degreaser and the Flare Gun (or the Detonator) in my loadout? Is the Flare Gun's afterburn damage reduced by 25%, or is it as normal?
Each individual weapon's special effect only corresponds to only that weapon, not the entire player loadout. It's just like although the Rocket Jumper has -100% damage penalty, you can still kill other players using Melee or Secondary Weapons (it's one of my favourite loadout - Rocket Jumper, BASE Jumper and Market Gardener).
So yeah, your Flare Gun will still have the same damage and afterburn damage as before.