The only thing I can think of is to start to break up the VTs being run (which scan config are you running?) against the target into segments until you can narrow down which VT is causing the problem. Divide and conquer, or start with the most suspicious VTs first? Do you have safe checks enabled? Are you including DOS attacks?
I guess that after identifying the specific VT that is causing the issue, to assess the .nasl script to determine how the VT interacts with the Tomcat server, can you debug Tomcat while running that VT?
ReInstall does not solve your issue, you need to find out (WHAT) exactly happens. Try to run a extensive log and check (WHY) your tomcat does not come up ? Maybe you have a serious issue with your installation, not only GVM might interrupt you tomcat but any other attacker can as well.
Tools like tcpdump and strace are your friend finding our what exactly happens. If you find this details you can see WHY your tomcat freezes … and then it is possible to detect the DoS and why your installation break.