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Get a real estate lawyer. NOW. Gather all of the documentation you were given at closing when you bought your house, and bring that plus the new notice to the lawyer.
This is something that was required to be disclosed to you before you closed on the house. Just about all states have disclosure laws when it comes to purchasing a home, and one of them includes any and all survey maps. Lying or omitting relevant information about the property (such as any wetland delineations, perc tests, surveying adjustments etc. performed) is illegal. Developers and sellers still DO it, but it is actually illegal in most states.
EPA may likely have nothing to do with it. Most of this stuff is determined by local committees, sort of thing.
Your lawyer should request, and receive, all surveying done prior to the development of the property; this is information that the developer WILL have, I promise you, although they might not be too happy to give it up. When you bought the property, was it all brushy type of woods, or was it landscaping/grass? If the developer had previously put grass down in the area, then the developer is the one responsible for destroying the wetland and must create some sort of remediation for it.
You can also have your own engineer test the area; in particular, perc tests are relevant, because if the soil perc's, then it's really not much of a wetland--especially with the 40 days of rain New England has been enjoying. I can tell you, all of our official wetland around here has been a freakin' mosquito factory, you wouldn't exactly mistake it for a flower-strewn meadow: More like a skunk-cabbage-strewn sewer. So you can challenge the 2002 engineer's designation, although that strategy is sort of dubious, sorta expert vs. expert.
Mostly the fault is on the developer for not telling you at or before closing. And since you were not told, they should be able to grandfather you in somehow--it's been non-wetland for so long, you weren't told and couldn't be expected to know, this is really the developer's screwup to remedy. Even if your lawyer cannot get the designation changed or get you grandfathered in somehow, they may well be able to get you a chunk of money due to misrepresentation of the property's use. I'm assuming you would not have bought a house with such a small yard, no chickens allowed, and so on, right?