If the system was working with the mixed wiring and then suddenly stopped working, it is obviously not the wiring.
You need to some basic network troubleshooting.
1. With everything disconnected from the switch but the switch connected to the router, connect your laptop to the switch and see if you get on the internet. If you do, then start adding connections to the switch ports until you add one and you lose internet connection. Then troubleshoot that cable and the device or devices attached to it.
2. Be aware, (and this is the bane of network topology), one device that is throwing garbage on the network can bring down the whole network and make all devices on that network inoperative. It's called denial of service or DOS and can affect VoIP networks as well. Use process of elimination to detect the problem.
Rcaman
