Sorry to hear of your situation.
Oil based stains contain solvents which typically outgas for months and sometimes years. The top coat used is water-based but still may contain chemicals that are not safe.
Low VOC and Green Guard certified does not mean 100% safe; it simply means it has satisfied certain requirements and met the standards of that particular organization.Unfortunately, those standards are not as high as they could be.
Your complaint is very common and needs to be addressed quickly. There are three possible ways to handle this:
#1. Sand off the finish and the stain and start over with a non-toxic water-based stain and re-seal with a clear non-toxic water-based topcoat. It is also the most expensive and time consuming, but its the best way to guarantee success. We highly recommend that you test any new product in a small area before applying.
#2. Apply an encapsulating sealer over the top of the finish. This may require two coats and it may not work perfectly. Part of the problem is that adding a new sealer adds water and water tends to re-hydrate the surface allowing off-gassing to continue underneath--sometimes even worse than before. It depends upon how well the stain and top coat have cured or dried. If they are fully cured, then an encapsulating sealer may work well, if not, then its better to wait at least three-four weeks.
AFM Safecoat Polyureseal BP is an encapsulating sealer that will block off-gassing and provide a durable finish.
- Tests in Japan on several AFM products have shown the reduction of formaldehyde off-gassing by 95-100%.
- The Polyureseal BP proved to be 100% effective after two coats.
3) Wait it out. Eventually the emissions of solvents and other chemicals will decrease and be undetectable. This does not mean there will be no effects. It only means the noxious odors will be less pronounced. Everyone has their own levels of tolerance to different chemicals. If you do not wish to subject yourself or your family, then I would choose #1 or #2 above.
For more information:
Also, read "How do you remove or encapsulate non-green wall and floor finishes?" a Q&A answered by Steve Rush.