You could just save the time you use to debug and then substract this whenever you need the millisecs.
An example:
Strict
Print MilliSecs()
Local time:Int = MilliSecs()
DebugStop
Local debugTime:Int = MilliSecs() - time
Print MilliSecs() - debugTime
An example:
Strict
Print MilliSecs()
Local time:Int = MilliSecs()
DebugStop
Local debugTime:Int = MilliSecs() - time
Print MilliSecs() - debugTime