BMW R1200cl warning and abs light flashing alternatly

Looks like you have a few issues there.

1. The battery warning. This is indicative of a weak battery and if your battery is 3 years old or more I would replace it.

2. If you have a weak battery this can trigger other warning lights in the vehicle, typically the ABS warning but sometimes other warning lights as well depending on the electronic features in the car. If you replace the battery this should correct the battery warning and most likely the ABS warning if both of these warnings appeared at the same time.
Normally, once the ABS warning is displayed the anti lock braking system(ABS) will be shut down. Whilst your braking will be normal, if you brake too hard and lock up your wheels on a slippery road there is no ABS assist to prevent the brake lock up which you have when the system is working.

3. If the alternator on the engine is not generating sufficient power and thus not charging the battery at all, or very little, you will likely get a battery warning light. I don't know if your 1999 vehicle has a warning light to indicate a faulty alternator or not.

4. Check Engine Light.
You suggested the CE warning has been showing up for a few days and before the battery and ABS warnings popped up.
The CE warning can be caused by dozens of different engine issues.
The vehicle needs to be scanned with the appropriate scan tool to see what fault codes the onboard computer is generating because if you have a CE warning light there will be fault codes generated 99% of the time.

Once these fault codes have been pulled the mechanic can start to diagnose the cause of the problem or problems. Each engine fault code your car's computer is generating can be caused by different types of problems so it is important that they diagnose the issues correctly. Otherwise your Check Engine light will remain on as long as the causes are not identified and fixed.

Very stiff pedal means brake booster isn't working. It's possible you have a master cylinder problem or just the brake booster. Battery light is separate issue,....
If you can, get the codes read from the computer and report back.

The ABS lights can come on for a number of reasons, not least of which could be the condition of the battery, although I can't think why it should happen after travelling 500 metres. You may just get away with resetting the ABS system, the attcahed link shows how ou can do this ith ABS1 and ABS2, what harm could you possibly do? (answer; plenty, but the narator seems to know what he's talking about)
BMW Motorcycle ABS II Reset

Codes can be removed from most mechanics with a code reader, they can check and reset them for you, bear in mind these lights came on for a reason, ask the mechanic what did the codes signify. Good luck

Check the ABS fuse. It sounds like the ABS electric pump is not working.

ok buddy, how long do you wont to live for???????
this flashing warning light is your ABS light!!!! like your brakes dont work right!!! look at the brake hydraulic fluid level, is it full up???? you could turn off your ABS by pushing down on No 3 switch along from the left on the lower switch pannel, but its your neck, also try starting the motor them put on both brakes (front and back) hold them on for a fuw seconds before you pull awaythis could reset the ABS, but get it sorted fast