There is a slight difference. The small primers may yield slightly lower velocity than the same load in large primer brass, but it seems to vary.
Shooting Times did a small test, not really a significant difference.
Fact or Fiction: Small vs. Large Pistol Primers in .45 ACP
Starline Brass did a bigger test and the results seem to vary depending up which test pistol was used.
Small Pistol Primers vs Large Pistol Primers | Rifle, Handgun, and Pistol Brass
Definitely keep the two types of brass segregated. A small primer will fall out of a large primer pocket, but a large primer can be crushed and that is never a good thing.