Yes, they can go flat, but that doesn't mean it's a genital wart. The vinegar test is not reliable.
The stigma of genital warts is worse than the warts themselves. Worse case....they're warts.....and in the grand scheme of life, it's no big deal. You get a prescription, strengthen your immune system, they go away and in most cases they won't return. They are just a speed bump in life. Sure a little embarrassing, but nothing to lose sleep over. After the warts are gone your body will keep the virus locked away in most cases and the likelihood of passing it along decreases. Just breathe. And as SkaterDave said, the vinegar test is worthless. Get checked.