It would be a shame to load a cartridge with a plugged flashhole when a decapping rod coul dhave prevented it. I guess the best way to look at it is if there is a process-related reason to remove the decapping rod (as the last poster mentioned), go ahead, but if not, you would be well served to leave it in as a mechanical check of the flashhole, if nothing else.
I am not sure what you are loading for but if you plan to prime before sizing keep in mind lube and primers dont always mix. It is generally advisable to order your process in a way that avoids introducing the primer to the case any sooner than necessary. The longer your components are in their raw form the better, in my opinion.
That's one of the big benefits of a turret press that I dont think gets talked about enough. Only 1 primer, 1 case, 1 powder charge and 1 bullet are ever in process at any given time.
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