Both flags are related to Trust relationships in AD.
It is very difficult to say what can go right/wrong without full understanding of the environment. What trusts are set up? What does the forrest look like? Are these flags being used Internally/externally/ both?
Microsoft Technet has a wealth of knowledge on these flags and others. Here is one link:
SID filtering quarantining is typically used to prevent attackers that have compromised a domain controller in a trusted domain to use the SID history attribute to grant themselves unauthorized rights.
There is a bunch of free baselines for Microsoft Windows Servers, Desktop etc have a look through those baselines, and register, there is some very good guidelines you can use for reviews and even some tools to check those baselines against as well.
An example of an updated baseline or benchmark is: