The red lights flashing means some type of control measure is taking control of your bike. abs, traction control etc.
If your charge is above 95 percent the bike wont regen.
If there is crap on the wheel sensor for speed, that can cause issues as well. given the lights are flashing tells me it is having a problem sensing your wheel speed.
Check both sensors, make sure they are tight, aligned, and there is not crap on them, like metal fragments or just grunge from the road. Check the wires, wiggle things a bit and make sure the wiring is intact.
The blinker lights might be an indication. There might be a short in the light, this normally happens when you have a cracked lens and water manages to get in there and cause some problems, or they get bent one too many times. The light can be working fine BUT there is still a problem. I have seen this where the problem only happens momentarily, ie something loose just taps the side or just for a moment breaks contact, and it's enough to throw the fault, (which will then lock the bike in that fault mode until it's reset / ie turned off then back on).
If it IS a short circuit that is causing that, that could also bring the voltage on the rail down enough where the ABS, which also works off 12 volts sees a bad power situation and goes into safe mode / shuts down etc itself, and no longer works correctly. You may or may not see that cascading fault.
Any electrical fault on the 12 volt grid can affect EVERYTHING that runs off 12 volts. If that something is some sort of electronic device, and not just a simple resistive load like a light bulb, then that glitch can cause problems with them
Id look into the lights, make sure they are tight. The bulbs are tight, and check the connectors on them, unfortunately I find that the connectors are prone to working themselves loose and the boards on IN the lights are not the best quality and can be damaged easily. Luckily replacement lights are fairly cheap.
Since the light fault is persistent, persue it. correcting it might fix the other issue, but check the wires /tightness of the sensor, and the sensor head itself for damage, foreign debris, and proper alignment.
Let us know what you find.
Aaron