Minotavr

Some time ago strange thing happened. I couldn't start the engine because the battery was dead. I charged the battery for about an hour, the engine started just fine, I drove the car with no problem aprox. 5 miles. That was in the evening
In the morning, the engine started just fine, but oops ! CEL on ! When I put her into gear, I couldn't get over 2000 RPM. Like I had a limiter. First gear - 2000 RPM, second gear 2000 RPM, third gear 2000 RPM and 15 Mph ! I managed to arrive to my garage, and noticed when the shifter was in neutral position I could rev it until 8000-9000 RPM. When in gear - limited to 2000 RPM.
I didn't touch the car for one day, but I fully recharged the battery. The second day I tried to start the car and...you guess, I suppose. CEL light off and the car worked perfectly ! I went to service and they put her on the tester, and it read ok. They told me because I disconnected the battery when I charged it, the CPU memory cleared and was no error code. Never happened again, but I worry as the car is an 43k 6MT from 2004 and way out of warranty.

Reading some threads about CEL on/blinking when in high revs, I wonder what is better for decarbing ? 9000+ RPM (and risking CEL on) or cleaning the engine regularly ? I must admit since I bought the car (6 months) I never exceeded 7500 RPM's. I felt like if i forced the engine could be an ... expensive move.