If so, you need to get to root of the problem.

Is it just cosmetic, or is there a risk of the roots damaging the foundation or sidewalk, etc.?  

Is removing a problem if roots decay over time leaving a void?

They are nice folks so I'm rooting for them.  

It takes root in the mind first before coming to fruition.

I don't really understand outside of who they're now paying how the existing lease wouldn't be valid @Shawn Root,  so please explain those clauses that wouldn't be.  

In any case, it's again "how to deal with a person with which I have a problem" (of which I'm the root cause, no less!).

For example, my lease states "Tenant shall be charged for repair of drain blockages or stoppages, unless caused by defective plumbing parts or tree roots invading sewer lines."

I guess, I find it interesting, that the idea seems to be rooted in how bad of a debt manager the person who file BK might be and then the idea to wait out another 5 to 7 years is actually the greater chance of that debt management practice to be right where they were prior to filing a BK.

From what I understand from your information is that everybody was pretty much up to speed on the dispute process but there have been some efficiencies put in place to better process these disputes and root out any fraud.