You should be fine. All entry points across the country are synchronized to use the same records, so any notes made in San Diego will be visible next time you enter, regardless of where you go.
That said, there is a (small) risk is that the CBP officer did not completely fix up your records, so when you leave the country, your exit is not tied to your entry. If yes, because the US has no record of you leaving, you might be considered an illegal overstayer and get stopped the next time you come. If you have proof you left the US, eg. an entry stamp into another country, you can sort this out on the spot; if not, things could get hairy.
In a sane country, this would be sorted out at exit immigration, but Uncle Sam doesn't have that. If you want to check, you could write to the CBP FOIA department and request a record of your travel to the US, which should show your entries and exits, and then you can (try to) take action if your exit doesn't show.
All that said, the mix-up with your niece sounds bizarre and confusing. As a wild guess, I'd guess somebody screwed up some data entry when they were processing your visa, although I still don't understand how they could possibly substitute your niece's details. Which visa do you have, and did she sponsor your application or something?