Is $3,000 to replace skylight flashing a fair price?

I got a new roof 2 years ago and had 8 skylights. The roofing company gave me three options: don't touch them, replace the flashing for $3k, or replace all the skylights for roughly $1000 each. I chose the flashing replacement option based on the contractor's recommendation since I planned to sell in a few years. Shortly after the work, the flashing came off one skylight during a storm, causing a huge leak. Another skylight recently had a small leak (about half a shot glass worth) during a heavy storm. These are the only two I could reach to photograph. I've covered two of the skylights in my bedroom because I got tired of dealing with them. I'm wondering if I should have chosen a different option or what I should do now. Can I have another company replace the skylights even if they didn't do the roof? The crew worked very late, until midnight, with limited lighting from a truck. None of them spoke English, but they worked very hard from sun up until midnight. I paid in full in cash.