As part of my planned food forest, I'll smother the existing grasses and (lots of) weeds with sheet mulch, on top of which I'll plant a nitrogen fixing ground cover (arachis pintoi). The problem is, every seed I come across is treated with inoculants (good) and fungicides (which seems kinda counterproductive...). Will sowing these seeds severely impact soil microorganisms? And could it affect bees once the plant produces flowers (neonicotinoids are known to be causing CCD)? Is there any method to remove the chemical coating, or should I stay away from the seeds altogether? I don't really care are organic certifications, it's an urban project.
Fungi-cide is really a bit of a misnomer; they are more like fungi-static -- as in the growth of fungi is slowed down temporarily until the compound is degraded in the environment. The only chemicals that actually kill fungi are things like bleach and hydrogen peroxide, by oxidizing the cell more than it can handle.
Solvents that disrupt the cell wall will also kill cells. The anti-fungal drug Amphotericin B falls into this category, since it binds to the ergosterol in fungal cell walls and causes them to leak. But Amphotericin B is a molecule that is produced by bacteria in their war against fungi, and it is too expensive to be used for a seed coating. Commercial seed coatings are molecules like thiram, a small organic molecule with a lot of sulfur on it, so that when it decomposes in the environment, the elemental sulfur is left around, which is fungi-static.
If you have some thiram coated seeds, it's not going to be problematic. Once the thiram decomposes, the sulfur could be beneficial in your soil and the soil fungi will readjust. If it makes you feel better, you could remove the thiram by rinsing the seeds with a solvent like acetone, but it's not really necessary.
Also, thiram has no relation to neo-nicotinoids, and it's going to decompose in the soil, not be transported up to the flowers.