The tools you use for troubleshooting are often referred to as troubleshooting tools. I prefer to call them data collecting tools. I’ve yet to see a troubleshooting tool that presents me with a dialog box, and tells me what the root cause of the issue is. All tools used to troubleshoot are tools that provide you with as much data as possible. Using your experience and knowledge, you filter through the data and can hopefully find the root cause of the issue. When you turn to these data collecting tools you’ll spend a significant amount of time digesting all the data.
Whatever tool you are accustomed to using when packaging a traditional MSI package, should and can be used for troubleshooting ThinApp packages. Here’s a list of common tools that I use. You may have others and you should be able to continue using those.