2001 forester s/ security light flashes while driving, stops when key is out of ignition or locked?

Had a battery go bad over the winter and got a new battery. The check engine light came
on when battery got changed but I figured it was just a code they could reset at yearly
inspection and emmision test. The security light also started flashing while the car is in
drive but once I park and take the key out or lock it, it stops? This also started since I got
a new battery. My car has been in the shop four days now for inspection and emmision
test, and I have a 8 month pregnant fiance here and am missing work. The garage can't
figure out how to get the check engine light to go off and stay off, and so my car can't
pass emmision testing. Wondering if I or they are overlooking something simple, but my
mechanic has a 2001 Subaru with the pancake engine and has over 300k on it so he
should know a lot about fixing them. Thank you