Multiple Vaadin servers in Eclipse project

I have multiple version of the vaadin server (vaadin-server-7.4.5, vaadin-server-7.4.6) in my eclipse-luna project configuration. I wish to only use the 7.4.6 version and remove the 7.4.5 version from my project. I traversed to the .ivy2 cache directory and renamed vaadin-7.4.5 .jar to .old. When I re-stared Tomcat I get the following error:

Error reading file

How do I remvove the old vaadin server from my Eclipse project without affecting the Tomcat server?