The two or three most common fungal diseases -- Early Blight (Alternaria solani), Late Blight (Phytophthora infestans) and Septoria -- live only on the aboveground parts of the plants, not in the soil or on the roots.
Early Blight and Septoria can overwinter on dead infected tops, but all you need to do is make sure every bit of diseased leaves, stems and fruit are removed from your garden by the end of the season. That will eliminate them as a source of spores that might infect next year's plants. Once they are gone, so is the fungus. If you get rid of the diseased tops and your plants still get infected again next year, it is from spores that came in on the wind from somewhere else or from infected plants that you bought from a nursery, not from your soil.
If the fungal disease affecting your plants is Fusarium or Verticillium, those are soil-borne and it would be worth looking specifically into how to distinguish those particular diseases from other problems so that you don't waste time and money replacing your container mix unnecessarily.
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