Despite tales of this problem being a one off, the internet reveals more examples of this failure, I would expect this problem will grow as bikes age.
Quote "I've got a low charge warning last Saturday and by the time I made it to the closest BMW dealership the battery was dead. The diagnosis was alternator failure, and this also killed the rectifier."
The problem wont be sorted by "Rinsing" the Engine after the event, The problem will be the Damage (Scoring) done from the debris in the oil from first noticing the fail to getting the bike into the dealers, and if rode long enough to flatten the battery as stated by OP quite a few miles must have been done
New motor would have been the way to go.
At this point I should introduce you to the whole story of my BMW R1200GS, which BMW claims, the two things have nothing in common.
In December 2015 I got my NEW 2014 BMW R1200GS LC (produced August 2014). During Dec 2015 I did maybe 300km and put the bike to garage (heated). Over the winter I started it few times (not many, 2-3 times). Everything was ok. In March 2016 the weather finally got better so I took it for a ride. Another 300-400km. Heated grips on as it was still cold outside. Put it back to garage for about one week. After one week I went for a ride, however, the starter would not turn with no indication in controls that the voltage goes down during start. Just no response to the starter switch. Got BMW Assistance to come over. When it came, we finally managed to start the bike using cables. That was before 1000km check at the dealership so at the time I put the bike for the checkup I mentioned the problem I had so they can check if everything is ok. Everything (according to them) was ok.
Since that time I had no problems up until the time when retutrning from my Balkan trip last July. The bike had 7,5k km already and my last-distance-home was from Albania to Poland approx. 1,5k km.
Everything was ok until outside temperature, after midnight dropped down to 7deg C. I had to swith the heated grips on. While driving the highway (already 1050km done) at around 140km/h suddenly the LEDs went off so I experienced blackout riding 140km/h on highway. The only way to have lights was to flash the high beam ( with many high beam responses from the truck drivers riding towards
) on the clocks all controls went on, ABS, ASC ... discotheque! The Voltage indicated 16-17V! When I switched off the grips it even went up to 18V! I pulled to the side line, switched on blinkers and drove for approx 3km for the closest petrol station. There I made a picture what Garmin Navigator indicated, (eng. tmp 98deg C so was probably the battery as I touched it - strange it did not explode!) and called assistance. Still had approx. 400km home. I decided that the road assistance takes me to nearest (Wien, Austria) authorised dealer / service station. When I finally got there in the morning (BMW dealer/service) they took my GS straight away for check (I was very happy!). At the station they indicated battery failure. Because of worldwide BMW warranty I thought it will be done under it but - they told me that my dealer where I bought my bike did not register my GS in european central base so they can not replace my faulty battery under warranty and I have to pay 160EUR for it. I called the representative from my dealer trying to find out what is going on? What I heard was to pay and take all documents with me so they (BMW) can refund me those costs when I am back to Poland. So I did, Austrian service replaced my battery, put my GS under 2h computer check if everything was ok and I could go further home. Arriving to Poland I took my GS to my dealer next day and left it for the checkup leaving all documents from Austria. Diagnose - all is ok. Took my bike and was happy for the rest of the season with another 10k warranty checkup around September 2016 (still no solution to my battery case). Now the funny part
in december I got BMW (dealer) written response that the BMW Motorrad headquaters will not pay me the cost of battery and service during my trip as it is difficult for them to investigate if that should be replaced under warranty ... crap! I was so embarrassed with their response that I let go of my quarrel. Since Sept 2016 up until 19th May 2017 I did another 3,5k km when the loose bolt thing in my engine happened.
Since I first heard strange noise (metal grinding) inside my engine and than noticed that there is no charging (batt V was 12,5) I made it approx 1km to the nearest parking so to call the assistance again. That was all distanse I drove with unscrewed bolt. Since I am not an electrician I was wondering if such damage (burned and swelled stator arms) could happen the year before, when I got 16-18 volts indicates of charging at time of battery failure or it happened due to unscrewed bolt and short circuit of the installation.
I asked for the written opinion (expertise) of an automotive expert and his opinion, due to the large amount of impurities that got through the grinding to the engine, is that it is reasonable to replace the shortblock in this case. The end (so far)...