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.