It sounds more like a zoning permit.
Do you need to submit a new one every year or only if the location of your garden changes?
If the cover would of been an issue, saying that a storm or wind just damaged it and you have to replace it I'm sure would of been a suitable answer.
More then likely if you weren't compliant for any reason at all, they would just give you like 10-14 days to correct the issues.
Do they allow indoor growing?
Do they require the same license/permit and inspections for indoor grows?
If they don't have the same requirements for indoor grows, then they really only care about the "public image" of it.