Yep, I had to deal with this twice. Once many years ago with a pop-up camper that was almost new, and a couple of years ago when I did exactly what you did, expect between trips.
Everyone will tell you NOT to do what I did, but this is what was recommended by the dealer when one of our tend ends got moldy on our pop-up.
Put a little bleach, may 1/4-1/2 cup in a big bucket of hot water. Fill another bucket with hot water. Use two soft towels that you no longer need. Soak one in the bleach water, ring most of it out. Soak the rest into the canvas where the mold is and lightly scrub. Do this a couple of times until the mold is gone. Then soak it to no end with the plain water. Soak it again. Take a third towel and soak as much residual water as possible. Let it dry thoroughly.
Get a can of CampDry and respray the waterproofing. If the seams had to be soaked reseal them with seam sealer.
In both cases this destroyed the mold and we never had another issue. In the pop-up there was still some slight staining. In our HTT the stains disappeared instantly.
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Chuck
2013 Jayco Jayfeather X20 E (sold)
2016 Chevy Silverado LTZ 2 Z71 Crew Cab (sold, and dearly missed)
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