Let me say this about that:
Thirty-some years ago I lived in Connecticut, and during that time I was chair of the Planning and Zoning Commission for the town in which I lived. The Zoning Enforcement Officer was also the Building Inspector, and I subsequently became licensed as a building inspector -- in Connecticut. So I speak with some knowledge when I say that the premise of that article is bullshit.
Yes, a building permit is required for a major repair. (In fact, technically a building permit is required for most minor repairs, but who's checking?) Yes, the Zoning Officer has to sign off before a building permit can be issued -- and under Connecticut law a repair to an existing structure, even if non-conforming, is ALWAYS allowed. Period.
The only potential fly in the ointment might be Federal coastal area management regulations, which MIGHT prevent rebuilding a home that has been destroyed without raising it above the mean flood elevation. But a home that just got waterlogged and needs to be dried out and get new sheetrock should not have that problem.
Don't confuse building codes with zoning regulations. The building code tells you how the building has to be assembled in order to be safe. That's all. Zoning regulations tell you how you can (and can't) use your land. I was blessed to be on a board with enough conservatives that we basically tired to just go with the flow -- big part of town was residential, the part that abutted the city was business/commercial. Within those there were the usual things such as distances from property lines, maximum building heights are areas as a percentage of land area, maximum sign sizes in the business/commercial zone. We didn't get into how short you had to cut your grass, but I know other towns closer to New Yawk (along what we called the "gold coast") were into that sort of micro-managing.