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The fly problem should have stopped immediately if, in fact, all the contaminated soil was removed. If you continuue to see fly activity over the next week or so, you may have to have a talk with the plumber. Any contaminated soil will continue to support the fly breeding.
Didn't you realize that when you had all those drain flues winging around your house that you've left all the drains in your house open for the flies to get into and lay eggs. Like you I located the source of the infestation, however, In order to prevent them from finding new breading grounds I had to close off,(seal) tall the drains in the house until I had to drain something. Then I sealed them up again. Then I went after them one at a time . I put up fly strips over the kitchen sink and any place I could se the little critters flying around. It took a month but now I'm clear. The very first thing you must do is find the source, in your case I'd start with the drains, Good luck. Tom