2004 Ford Explorer

My 2004 Ford Explorer stopped starting after I
replaced the 9 yr old battery. I noticed the theft
light rapily blinks when the key is in the on position.
I read alot about the PATs system and the issues
with the no start it iscauseing with this particular
vehicle. I tried resetting the key and read that I had
to take it to the dealership. So once I got it there
and explained it to the lady assigned to my car she
looked like she had no knowledge of the problem.
She called me back and told me $500 for a new
alternator and that she did reset my keys due to
trying to start it over and over again. She said the
theif light blinking was from a bad connection. Not
sure what she meant. It had a brand bew battery
and when I asked if it was the alternator
connection she said no, its fine. Does this sound
right? I fear I'm losing $500 from her trying to sell
me on somthing I don't need. Maybe I'm paranoid
that she is covering up the PATS issue, or I feel she
is not as experienced with her young age.