The "sealing" on commercially purchased jars is not sufficient to imprint or damage the flats in any way. If you look at a used lid from proper canning you will immediately notice a deep imprint caused by the heat and vacuum sealing.
I've actually used new lids for vacuum sealing with my FoodSaver and the lids were still viable for canning since the rubber seal was not depressed permanently by a heat process.
Use your new lids from the jars with confidence.
Support bacteria. It's the only culture some people have.