I know that this was an issue on my ThinkPad W700 with Linux installed. In Windows, the Lenovo drivers would automatically manage the charging level to preserve battery life, but in Linux it would overheat when plugged in for extended periods of time, and I suspect that it was "over-charging". Within a year, the battery had about 50% capacity, and a replacement battery degraded as quickly.
My current ThinkPad w540 does not seem to do this in Linux, so I suspect that either Linux or Lenovo has solved the problem, but I haven't really investigated what happens. I leave my ThinkPad plugged into a dock most of the day at the office like I did with the W700, but it's battery still has almost full capacity a year later and can still keep it running for 5+ hours on a full charge. (Linux could never get the 7+ hours that it can get under Windows and I haven't run Windows for more than 1 hour in almost a year.)
I'm pretty sure that the charging logic is built into the battery or other dedicated charging circuit hardware. Almost positive that while the OS can say "don't give power to the battery", it can't say "give power to the battery even though the battery says no". Not a great source, but this agrees: http://computer.howstuffworks.com/laptop-battery-overcharged...
My current ThinkPad w540 does not seem to do this in Linux, so I suspect that either Linux or Lenovo has solved the problem, but I haven't really investigated what happens. I leave my ThinkPad plugged into a dock most of the day at the office like I did with the W700, but it's battery still has almost full capacity a year later and can still keep it running for 5+ hours on a full charge. (Linux could never get the 7+ hours that it can get under Windows and I haven't run Windows for more than 1 hour in almost a year.)