You probably need to add entries to the PendingFileRenameOperations exclusion list, so the systems are not flagged as ‘pending restart’ when there are entries there; then the systems would only flag as ‘pending restart’ based on BigFix actions, not because something else on the machine is flagged as Pending Restart.
Have a look at the this thread for details:
To exclude everything in PendingFileRenameOperations, you could send an action for
setting "_BESClient_ActionManager_PendingRestartExclusions"=":;" on "{parameter "action issue date" of action}" for client