According to this Knowledge Base article from Microsoft it only prevents
Autochk.exe from including the drive for a
chkdsk /f during start-up.
Every time Windows restarts,
Autochk.exe is called by the Kernel to scan all volumes to check if the volume dirty bit is set. If the dirty bit is set, autochk performs an immediate
chkdsk /f on that volume.
The chkntfs /x commands are not cumulative, the command overwrites any previous drive exclusions that have been established. In the above example, chkntfs only disables the chkdsk checking on drives D and E, drive C is not checked for the presence of a dirty bit.
So it shouldn't prevent the dirty bit from being set when there is a problem. You should however check the drive regularly for this dirty bit if you exclude it because you don't get a warning at start-up anymore.