Reversing the main power leads can destroy all the FETs, and sometimes the capacitors, and the LVPS parts that create the 5v, 12v, 15v, etc that runs the controller brain. That level of damage is typically not worth the time and money to fix, and is cheaper and much easier to buy a new controller.
Sometimes with a momentary reversal, you get lucky and nothing is actually destroyed, but the damage done to them from the stress may cause failures later on under load (when riding, etc). Sometimes no damage occurs and it lasts for many years just fine (but this is not really typical).
If they were left reversed for any length of time rather than a simple momentary accidental reversal, the capacitors may be damaged if not destroyed, and the battery current shunt may even have unsoldered itself or heated up enough to damage the PCB around it (or make solder run around inside to short other things out and blow up more stuff).
There is info on testing FETs in various places on the forum, and at http://ebikes.ca in the Learn - Troubleshooting section.
For the flashing light, you can check the controller manual (if it came with one, then that, or the seller page for it if not, or if they don't have one, you can try QSMotors or other sellers of the "brand" and see if they have one that matches your model and version, so that you can find out what the specific error code is.
There may also be info on it in one or more of the many Sabvoton troubleshooting threads or posts here on the forum, if you have the time to look around for them.