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Your Dr can do the filling then try in your aligner to make sure it fits. He can adjust the filling to match the aligner if he needs to so not to worry....
As long as the filling follows the contour of your original tooth, which it should, then your invisalign trays should fit fine after the filling is done. I would bring your invisalign trays to your visit for the filling and try it on after the filling is done, with your dentist still in the chair. This will enable the dentist to adjust the filling and/or trim it down so that the aligner will fit. If the filling is very large or your require a crown it is highly likely that your aligners won't fit and then you will need to get new aligners made.
We prefer to have the aligners in for anything except eating or chewing gum, brushing and flossing of course. Please stop smoking, this may be the greatest time for you to give it up. Good luck, you can do it.
Remember its all timed so if you stop now and start up in two weeks you will finish at least two weeks later. There are some treatments that can be done during and after that are covered by your Dr and invisalign that if you put off your treatment too long you will sometimes it will cost you...
Unless the sport requires a mouthguard it should be fine to wear your aligners. They hold so well to the teeth that they are unlikely to come out if you fall or get bopped in the head. But if your sport requires a mouthguard (football, wrestling, basketball) than just remove you...