While I can't say if the mechanic hooked things back up to try to put the blame on the amp... a 1200w amp can destroy a factory alternator.
I did car audio for 8-10yrs as a living. depending upon the amp and the load that it pulls it can put heavy strain on the alternator.
If you are running your system hard and seeing your headlights or dashlights dimming when the bass hits, this is a sign that not enough power is being created to keep the amp running at 12v. Which means your factory alternator is under a hard strain to recharge the battery.
You can put a band-aid on the system such as a capactitor which is run in series between the power and the sub amp. However this won't resolve the problem as the capcitor can only store so much energy and in music which uses alot of bass notes it won't be able to charge up and you'll once again be putting a drain on your amp. Other option is using a second battery such as a gel-cell or a deep cycle marine.
As noted above look at a high-output aftermarket alternator if you are running your stereo system hard for a long term fix.
If you don't mind me asking, what is the fuse rating on the Amp itself and what is the amp and the model? If you have your spec-sheet for the amp look at it (or the manufacturers website) and see what the load pull is. Then look and see what the output of your alternator is. You'll want your alternator to be able to put out more than what your amp is pulling, ideally 25% more.
You can buy a branded after market alternator like Stinger, but look at big bucks... try seeing if you can have your alternator rebuilt, but to a higher spec by a company who does this, will be cheaper and it will bolt back into factory location without any mods, after market upgrades can often require adaptors.
good luck resolving the issue.