The following parameter will turn off MFG's permissions migration logic, which should allow permissions granted in Exchange after the initial migration to remain intact:
The following information can be found in the MFG INI Reference Guide, which is available in the Documentation directory of the software download:
boolean; default = 1
ACLs=0 tells the program to not copy ACL information to Exchange during the migration. By default (1)
the program will copy ACL information and will set folder permissions in Exchange.