I had a similar problem. I had a prject referring to a no more existing Tomcat instance. I was not able to remove Tomcat from "Server" and "Runtime Environments" from UI (delete button always gray),so I solved the problem deleting all the reference from the filesystem:
In project folder check files:
.classpath
.settings/org.eclipse.wst.common.project.facet.core.xml
In workspace folder check:
.metadata.plugins\org.eclipse.debug.core
.metadata.plugins\org.eclipse.wst.server.core
.metadata.plugins\org.eclipse.core.runtime.settings\org.eclipse.jst.server.tomcat.core.prefs
Maybe a bit brutal but I didn't find a better solution.