Faulty construction is an EXCLUSION (caps for policy language).
Homeowners insurance on DWELLING and DWELLING EXTENSION, works like this: you are covered unless the CAUSE OF LOSS is SPECIFICALLY EXCLUDED. In this case your cause of loss is specifically excluded. To elucidate you further, coverage on PERSONAL PROPERTY usually works in the opposite way; you are NOT COVERED unless the LOSS was caused by a NAMED PERIL.
Filing claims works like this: your carrier can drop you for claim FREQUENCY (number of claims per time period). They can NOT drop you for claim SEVERITY (cost of your claims). Filing two claims in a short space of time does allow them to JUSTIFY (to the state insurance commission), dropping you. Once dropped, you are essentially on a black list for other AAA rated carriers, NOT SOMETHING YOU WANT TO BE ON (that one was for emphasis)! Claim FREQUENCY includes claims for which you were denied, or paid very little. Simply notifying either the home office of your carrier or their agent of a loss is considered FILING a claim.
Your roof claim was covered because the faulty construction lead to additional COVERED damage. If they paid to replace your roof, it was to save them money in the long rung, or more likely, because it was necessary to fix the covered damage, i.e. to get at the damaged framing, they needed to remove the roof, or both.
I worked for years in property insurance claims for American Family Insurance Group. I highly suggest you never file a claim for under 10% of you combined average annual household income.
P.S. your agent is most likely CAPTIVE (works exclusively for the carrier), and as such, must do as they tell him to, including dropping you even against his wishes; even if he was your brother/father/spouse. Also, agents have one function, SELL. The rest they don't understand so much. Older agents may have been dragged into a few claims in their day, and learn a thing or two about how the home office works in such events, but let me tell you something as honest as the day is long; agents are terrific salesmen, and can smile at you while they tell you they killed your mother and ate your children, but even the best agents don't know doodley-squat about claims practices, technically.
P.P.S. Two carriers, Chubb, and Fireman's Fund, are non-confrontational enough that they pay claims they do not legally have to, to keep their EXTREMELY WEALTHY AND HIGHLY EDUCATED customers happy, but unless you have either of these FIVE STAR carriers, expect to be denied.
P.P.P.S. When your carrier pays you and then tries to collect money from a third party (such as your ex-roofer [who hates you now]), they are initiating a process known as SUBROGATION (not misspelled, and pronounced - sub-row-gay-shun). It is important that you know this, because if they do collect from your ex-roofer, you are entitled to your deductible back (in so much as they recovered). The deductible is the FIRST DOLLAR of a claim, and if your carrier collects, since you paid the FIRST DOLLAR, you get the FIRST DOLLAR back.