I've actually changed the substrate in my 20gallon with fish in the tank. I used a dog food scoop to remove the flourite, then vac'd after I let the dust settle, then added the eco complete.
Keep in mind, this could cause a mini-cycle, depending on how much surface area you have in your mechanical filter media, number of plants, and fish load.
Also, flourite only supplies iron to the plant roots...flourite in itself isn't a wicked fertilizer...but it has the ability to trap and hold mulm and root tabs and make that available to plant roots. In other words, flourite isn't going to affect water column dosing of ferts. However, since you'll be replanting the plants...they'll go through a bit of a 'shock' phase. I'd say you'll wanna wait a couple of weeks before you start doing any kind of macro dosing. Some good root tabs, however, wouldnt' be a bad idea right after replanting, if you have heavy root feeders (like swords and crypts)