I've got a whole bunch of brass with those larger flash holes. Winchester says you can use them with standard loading data for the .45 ACP, no problem. However, Winchester also advises that the ones stamped WIN NT 45ACP should not be reloaded.
It is not that the brass is deficient in any manner, but the primer pocker made for the small pistol primer, rather than the standard large pistol primer. Should one of those cases get mixed up wityh regular 45 cases and you try to put that large primer in that small pocket, well it won't be pleasant. However, you can reload them using a small pistol primer should you so desifre. I have a Colt combat Commander that won't shoot worth a tinker's damn with anything. Yet, when I loaded up the few small primer pocketed 45 cases I had on hand with my normal target load of 5.0 gr. of W-231 and a 200 gr. SWC, that gun shot the tightest groups it has ever given me. No pressure problems and they worked just fine.
I would say that if one has a couple of hundred or so of them, go ahead and load them being careful to keep them separated. If you have only a few, crush them with a pliers and toss them.
If the larger flash holes bother you, go ahead and toss them, but IMHO they're OK to load and shoot.